That could eventually become a big problem for TCs that are at all focused on multiplayer. Hell, I'm already running close to 30 squadron logos just from what I've picked up playing FS2 multi. Everyone who plays a lot will eventually want to use their own custom pilot images and squadron logos, and with the automatic transfer they will end up in the folders of everyone who plays. In short, if we look a bit into the future, 64 is way too low.
That does pose another problem though. Even if the limit is raised or made dynamic, it will quickly become very cumbersome to find the logo/image you want by scrolling through a list of 100+ that only displays one at a time. So ideally something to address that would be nice as well, though I'm apparently in an idea-drought at the moment as nothing's coming to mind.
[Edit] Maybe some way to select between official, transferred and self-made images would solve the navigation problem. It would require some extra subfolders under data/players/squads and data/players/images to keep them seperate though, as well as an interface art change to add the selection buttons, plus of course the code to make it all work. Not exactly a trivial change.