You mean Hardening as in the spell? It's a money sink itself that basically just protects from bumps and scuffing. A sufficiently determined person can smash through it without too much difficulty, or use the falling damage trick: 200'= 20d6 to anything. People also love Adamantine weapons, which while not perfect (they only smash hardness of less than 20, which means 19 or less), will still wreck any Hardening-'d items without serious caster level or Mithral starting hardness.

Hard objects are pretty difficult to destroy with un-optimized AoE damage, but there are still monsters and spells that can do it. It's more that a lot of items can be easily destroyed by wanton blasting-while some magic items say they're mithral or adamantine, and magic weapons/armor get some bonuses on top of their larger hp to begin with, most do not. It only takes 22-30 fire or electricity damage to break most steel items, or just 2-12 for weaker materials. That's not counting if they catch on fire, and acid or sonic only requires half the damage even if the spell doesn't explicitly bypass hardness. Many oozes also ignore damage and just annihilate gear on a failed save.

Infinite traps and spell clocks are on my list of "not even worth considering," but obviously you just fight fire with fire and make your entropy devices infinite. You basic matter creation (Water and Walls) creates far less than a 10' cube per casing, which is your standard matter destruction. A sufficiently souped up Wall of Fire can incinerate quite a bit even without being permanent or infinite.

For speed of income, you can if necessary simply interrupt them. I believe I brought this up in a previous thread (you were probably there too), but the existence of divinations that can contact the gods and gods that can see the future (any greater deity), means that the DM can justify having your operations attacked before they've even begun. Essentially the only way to hide from a god is with another god, so you need DM approval to hide your doings. Of course you might have trouble justifying where you're getting all the encounters that are capable of finding and attacking PCs who've managed to hide from everything short of the gods, but if the PCs are trying to go small-scale infinite well the DM has an infinite number of infinite planes from which to draw Schrodinger's NPCs and outsiders.

And if the question is actually being phrased in terms of crashing the economy, well the DMG already says that's under direct DM purview. The most you can really justify RAW is draining the ready cash out of a population center, then possibly buying everything out from under them, which still assumes they're robots who are forced to sell to you.

Someone wanted a more direct guide- I'ma go down the list one by one. there's not always direct magical "counters," but there's plenty of "weasely" things the DM can say to counter the players weaseling even before just saying no.
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Animate Dead: "Creeping darkness effect" LM/BoVD states that creating undead leads to more spontaneous undead, threatening apocalypse, entire classes and organizations are dedicated to eradicating undead. A single casting of Celestial Brilliance (BoED, 4th level) on a rock lasts for a week and annihilates puny undead in passing, all you have to do is get the rock in position.

Water to Acid: The acid created by this spell is actually superior to PHB acid in that it destroys metal, but this means they are not equivalent and thus there is no RAW price you can try to sell it at. Like any liquid, smashing the containers effectively ruins the stock-and possibly a lot more around it in this case.

Distilled Joy: The casting time vs/income of this spell is no disastrously problematic, at 50gp/day you have plenty of time to throw plot at them before wealth is out of control. Attempting to abuse it via infinite casting pleasure dungeons is likely to attract the ire of every Good deity (and the main market is Good outsiders). Paying for a properly cushy lifestyle for your "blissful" cattle will eat into profits. More importantly, the existing item for the evil counterpart explicitly keeps the day long extraction time with a whopping 64,000gp cost, making it doubly obvious any infinite scheme is the DM's own fault. You can waste it as easily a smashing the container and leaving it spilled upon the ground, and as a pile of Permanent magical effects they're easy to detect without further countermeasures.

Fabricate: Has sharp limits on volume, limiting what you can do with it. The most reliable value you can get is converting raw materials into art objects (a trade good) to triple your money with each iteration, and yeah there's not much counter to that aside from actual market forces depressing the value of art over time. You can play dumb with NPC traders who lack the Appraise skill to valuate the art objects and thus refuse to accept them for anything more than their raw materials worth, resulting in no wealth gain (and that applies to all the commoners those traders trade with too)- or who pretend to play dumb because they're in league with/don't want to anger the craft guilds you're trying to shove out, since when you leave they still have to deal with those people.

Lyre of Building: This provides only rough labor, which is at a bit of a premium in a medieval 90% farming economy, so it's not really stepping on anyone's toes- but it also doesn't create much wealth. Unless you can convince someone to "buy a bridge" off you, buildings are very valuable but the only serious "buyers" are the people you had to buy the land from in the first place- you do remember that the king owns all the land, right?

Plant Growth: This spell is grossly overestimated. It increases yield by 30%, but since yield isn't defined it doesn't actually do anything. Either there's a bunch of extra food of indeterminate value, or you make 30% more gp off your farming checks, or the DM decides it suddenly uplifts the setting by shifting farms to trade jobs. None of these are RAW, so trying to claim it has RAW impact is laughable. Regardless, this is where "anything that eats more than it should" comes in, with countless supernatural monsters (and spells that can summon them) that ravage crops. A single monster could easily reduce the yield of a region by 30% or more, making Plant Growth a requirement to survive rather than a luxury, and that's without even killing the peasants directly.

Portal to infinite materials: The only planes of infinite materials with a RAW justification that I'm aware of are the Elemental Plane of Earth, and the first layer of Acheron. Prospecting on the plane of earth gives about a 5% chance every 8 hours of finding a valuable metal (avg 22,000 over 22 hours of further mining) or uncut gems (avg 3,025gp after gemcutting), with an equal chance of finding an elemental pocket or chamber that could contain an encounter- and the digging rules don't actually preclude separate random encounter rolls (which RAW don't go lower than 5% per hour, call it 44% per 8 hours for .95^8). The given encounter table is around EL 10, which is 5,800gp per encounter. With around a 50% chance per mining roll of an encounter but only a 5% chance of loot, you're facing plenty enough encounters to make up for any mining you do.

Acheron is similar: while the plane is made up of floating iron cubes, you'll need time to harvest that iron, and the DMG gives an EL 15 random encounter table, so unless you can harvest more than 22,000gp per encounter you're not breaking the bank. A cubic foot of iron is worth 49.1gp and weighs 491lbs, and you have to get it back to the material plane or wherever you're selling it-you're probably doing better than Distilled Joy, but at what risk?. Being a plane that's at constant war it's also less likely you'll find a place unpopulated enough to roll for minimum encounters.

True Creation: trades xp for gp, unless you're ignoring the cost with something else, which is a problem with something else rather than True Creation.

Unseen Crafter: this is another one that has no particular counter aside from simple market/opposition/supernatural pressure. Technically it can't make weekly gp checks, but if you set it to creating art objects of arbitrary value to guarantee it finishes them you pump out a stream of trinkets that triples your value at the rate of approximately (10+skill mod)^2/10 per week, *spell slots*caster level/7, (roughly 30-60gp * how many weeks worth of crafters you cast in profit per week as long as raw materials are available). At level at which Unseen Crafter becomes available you can make a useful amount of money off it, but Fabricate still beats it.

Wall of Iron: at cl 12 for efficiency, you get 75 cu ft of iron for 3,632gp, assuming that it can be melted down and used as normal iron. Unfortunately this is not what the spell says: it instantaneously creates a flat, vertical iron wall that is subject to rusting, perforation, and other natural phenomena. It does not say that it creates a volume of recyclable, tradable iron. The DM can simply rule that the Iron Wall created by Wall of Iron is not suitable for any purpose other than what it's created for, fluffing it however they wish. As for magically destroying it, a single Rust Monster can destroy a 10' cube of iron per round, making it explicitly useless. A fire resistance/immune Rust Monster could even go after the foundry. The Rusting Grasp spell isn't much of a substitute, but an acid substituted Wall of Fire probably doesn't leave much of use behind.

Wall of Salt: same rulings as Wall of Iron, except you can destroy it via water effects rather than Rust Monsters, if you're using that motivation rather than simply ruling against it.

Wall of Stone: while I said myself that you can make valuable buildings with Wall of Stone, the problem of buying the land to build it on and then who you're going to sell it back to remains.