Just a quick question. If I clear out a cave, fort, etc. will enemies respawn? and how long will it take?

Yes, they respawn after a few days, maybe a week. And even traps and treasures will respawn with them. But I am not sure if there are some dungeons which will not do this, usually, they do.

http://www.uesp.net/wiki/Skyrim:Respawn

Some forts doesn't respawn with the people you wiped out but they will be taken over by civil war faction depending on who rules the current hold.