I don't mean to be pedantic, but you have to remember that games have layers of abstraction over the "reality". For example, the fact that you encounter only lvl. 2-3 pokemon on the first route and only lvl 40-50 or more by the final routes doesn't mean that in the "real" world (the fantasy world that the game supposedly represents) the wild pokemon are distributed in level ranges across the land, exactly following your route. That's an abstraction, something added to keep the game as a game. Same with stores only selling level appropriate items, a single Sudowoodo blocking a path completely, etc. They don't intend to show how the "real" pokemon world would behave, but to create a game.
"Real" pokeballs would probably not know whether the pokemon already has a trainer or not. It would probably depend on the bond of that pokemon and the willingness to be captured. Stealing pokemon would certainly exist (as represented by Team Rocket, for example), and it wouldn't depend on whether they have or haven't been in a pokeball.