No more than 128 files/folders DIRECTLY (aka not recursively) in one folder. So you might have, let's say, 200 ROMs: you can't put them all under the "games" folder directly, but you can have folder "part_1" and folder "part_2", both under "games" and containing 100 ROMs each.
Also, remember that each ROM will have its save file, so it doubles the number of files.