Do these guys ever respawn in any of the dungeons? If not, is there a way to reset a dungeon so they are not empty?

Some do and some don't.

I've got dungeons that I did really early in the game that never respawn. And then I have others that respawn all the time.

I think thy're all supposed to respawn. They just don't. Glitches!

It's supposed to be 30 game days, but some say visiting the dungeon or area around it within that time resets it.