I think an in game day is an hour in real time. Pretty sure there's 3 bank deposits per in game day, and they're 20 real minutes apart. That'd be an hour.
Some missions seemed to skip me ahead in time, though I'm not sure about this, I've only played it through once. I know when I let a captain get away, I'd just go play some story missions until he came back. You do get a message when they return, as the fella above said.
To stop captains getting away, I think it's best to take over the entire roof area around them. Kill every guard with assassin's signals, knives or crossbow(without being seen). Then stay on the roof until you've found him with eagle vision, and can get a clear shot with the hidden gun. Most guards run away after you kill him, so it doesn't matter that they hear the shot. Don't forget to search the captains body too, they have a good haul.
If you're still having trouble, you might consider saving the game before atempting to kill a captain, then reloading if you fail. Though I think you should be alright if you kill every roof guard and just be patient.
Edit - I tried to edit this last week, but it seems it wasn't accepted by peer review or however it works...anyway, when you want to save the game, just check your assassin pigeons, or craft bombs, or buy something. The auto save goes off whenever you do anything, pretty much. So just take advantage of that.