Do unconscious victims wake up? How long does it take?

No one gets up when Corvo is done with them.

But!

On the console versions, there is a limit of around 5 unconscious/dead people in a given zone. So when you go and add another the set one will disappear.

This isn't an issue for corpses if you buy the disintegration upgrades.

The personal computer version(s) may allow more bodies about due to the higher memory availability.

So what this means is that you must hide a body immediately (or leave it where rats can't get to it) if you are going for some kind of bonus or low chaos, as the opportunity to do so will be gone later.

Enemies don't wake up in general sense, however their bodies are known to disappear from the game to prevent the memory usage, bugs and other possible issues.

I'm not sure if they disappear when the maximum amount of bodies is hit or when you get too far away from them.

In my playthrough I haven't noticed single disappearing or reappearing guard, mostly because I played fast and without unnecessary returns.