As for why people live in the shrines: Someone have to run the shrine, keep it tidy, do the dishes and so on, and it's not like they sleep on the altar :P Of course, that doesn't explain why they just hang out instead of busying themselves with daily chores.
The ones outside could be mistaking you for a worshipper, but then it dawns when you kill the rest of the staff
One thing that worries me however, is the way the thugs out in the wilderness just dope around at the same spot, night and day. Shouldn't they be around, doing thugs' stuff? Or is it the deal with the local authorities: "As long as I stay here, they know where to find me, and we all go on with our businesses. Hand me your money"? Ok, so one or two of them happen to have a den somewhere near, but the rest of them...?
Seriously: One thing that would have been cool, was if some of the critters also hunted other critters for food. Is that too much to ask?
Also: Talking about food and water. In "Eye of the Beholder" you had to keep an eye on the rations. I miss that bit in the TES games. Going over the mountains for weeks without anything to eat or drink is kind of hard to take seriously. Ok, so you could eat the rat you just killed, but it just isn't the same.