Walt, if you have a script that creates the mod package, I'd suggest adding a command that removes any "empty" folders, or rather folders that do not contain *.ship.png
files (including subfolders).
An odd thing I noticed is that some users have png files that are not ship.png files. One user - sorry, forgot which one - has a png file that actually looks like a ship, but the game does not recognize it as a ship if you rename it to ship.png. There are also a few users with incomplete and invalid ships - with disconnected thrusters and such...