They use the same formula for DCs as PCs. This might be an area where you want to tinker with the NPC depending on the level of the party, rather than just using the automatic scaling. For example, if you reuse a stock evil wizard for a minor villain at higher levels, give it a bump in Cha or a few more Spellcasting feats.
This. If this NPC caster is supposed to be a big deal, just go ahead and give them a bunch of spell casting feats. Even if they're not supposed to be a big deal, I would still recommend giving them 1-3 depending on TL. If you really don't like the idea of giving NPCs lots of feats you can just jack up their charisma, but I think the feats method is preferable to that.
If you're comfortable with a small house rule, you could just spend xp directly on their casting DC. +2 DC for 3 XP would be in the neighborhood of reasonable, but I think that would result in sort of bland NPCs.