Breath weapons are supernatural abilities for dragons...

[atemu1234]

... so why do most templates saying, "the base creature loses all supernatural and spell-like abilities" such as sanctify the wicked's template that use a dragon have them keep their breath weapon?

[Albions_Angel]

Probably for lore reasons. For example, they are classed as supernatural abilities but on dragons that are based off of European dragons they are probably natural. I would argue that such spells that strip supernatural abilities would work on Lung dragons, which dont have breath weapons, but do use spell like abilities, with 3 dragons being able to use breath like abilities. Other dragons probably generate their breath weapons in another way. Like fire being generated from methane build up and a spark box.

[Chronos]

Because the authors of D&D screwed up almost every example character or creature they wrote.