I apologize if this is something I should know already, or if it's been asked, but I did a quick search and didn't get any results.

Do knocked out enemies eventually wake up?

There's been several occasions where I've knocked out ALL guards patrolling an area, but when I reload the game, the bodies
are gone and shortly after the guards re-enter the area and resume patrolling as usual. Like, for example, in the Overseer's
building.... I knocked everyone out on second floor, stashed bodies, and then later had to reload.... and when I did, all the enemies
were back like I never took them out in the first place.

Is this supposed to happen, or is it a glitch.... or is it difficulty-dependent?

That would be a glitch. Enemies that are KOed never actually wake up.

They are supposed to stay unconscious, so it sounds like a glitch to me.

Dang it, I was afraid that it would be the case.

Same here I put all that effort into being stealth and putting them unconsious then reload and there back. So i'm guessing killing them too won't help?

Thats sounds like a glitch. Unless you are accidently reloading from a early save.

Only time more guards appeared for me is when I knocked out everyone on the first floor in the Golden Cat. A guard wandering from his patrol walks in, and says "Why isn't anyone patrolling here", he looks around the room a bit more then says "This is strange" then leaves the room. A couple minutes later he comes back with three other guards, telling them "I'm telling you something strange is going around here, search the area". And personally I think thats awesome.

Ah, now, Sour, this sounds like a possibility in at least one case.... a guard walked in, said "This is a restricted area, why isn't anyone standing guard here?" and walked off.
When I returned later, there were more guards in the area, so maybe.... in some cases, I missed someone going for reinforcements?

Thats a possibility, but I'm not sure if they pull reinforcement from an infinite pool or go to the other guards in the area and bring them over to the suspicious spot.

Oh, I just remembered, the building where you get the poison for the distillery, I had cleared the guards in the area before it. Upon returning from doing Granny's dirty work, there were more guards but on a more strict patrol, there were guards in their normal positions as well two guards walking around the area together. It could've been that a guard decided to wander from their normal patrol (which happens often, they even talk about it sometimes) saw no one around then ran off to grab more guards.

They never wake up for me, which is good, it probably doesn't help that sometimes I throw them off of high places even when they are sleeping. Yet I still get the lowest Chaos rating. Only two times did it ever reach, "High", the beginning and the end, oddly.