Thing to bear in mind is that the passage of time in this game is tied inexorably to story progression (consider the constant presence of the merchant who constantly says he's going to leave soon but never does, as the sun never sets no matter how long you let the game idle), so as a result, unless there is a specifically good reason for enemies to respawn (as would be the case with Mook Makers), once you've wiped a map of enemies, it makes a lot of sense for there to be no more enemies on that map for the rest of the "day," at least. Again, tied inexorably to story progression.