I have a theory on the Moldaver plotholes. It's mostly head-cannon, but I think it fits. But I haven't put too much thought into it, so feel free to tear it to shreds if you can find some inconsistencies.

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I think Moldaver worked for Vault-Tec. It was never specifically stated, as far as I remember, but she seemed to have intimate knowledge of what was going on there in the past (claiming to personally know Cooper's wife and having seen a side of her that he was not aware of). I'm not sure if she infiltrated them with intent or if she was an earnest employee who learned the truth about how horrible they were and decided to betray them. Either way, she was working against them from the inside.

So I suspect she actually was frozen with the rest of them in Vault 31. At some point she was thawed and put into Vault 32. I suspect she fled the vault and integrated into the NCR, climbing the ranks there. Maybe with the intent of using them against Vault-Tec some day, or maybe she was just trying to start a new life. That's when she met Rose. After Hank retrieved his kids and nuked Shady Sands, she put together a band of raiders, used Rose's Pipboy to access Vault 32, and revealed to them the Truth (tm). Which caused mass panic and hysteria and they all killed each other and themselves (not sure if that had been her intent or not, but it happened regardless).

In any case, she took over the now empty Vault 32, sending telegrams to the other two vaults that she had been elected leader after the previous one tragically died. This explains why Hank didn't freak out when he saw her. It's possible he had no idea she had ever left Vault 32 in the first place, since it was made clear the three vaults don't communicate all that much directly. As far as he knew, she remained in 32 and was eventually elected leader since, 'when things look glum, vote 31.'

Admittedly there are still some minor holes here, like why did Moldaver infiltrate 32 instead of going straight for 33? (Maybe she had originally intended to use the 32 Overseer for her plan, but when he was killed, she made a new plan to get into 33? But considering Hank was Overseer of 33 and she had a personal grudge against him for nuking Shady Sands...I'm not sure why she would not have wanted to use him in the first place.)

But this theory does at least fill a few of the holes.