I think it might have something to do with copyright laws. There is one copyright law that states that if you don't excercise your copyright, you may lose it.
In other words: If Nintendo lets someone use their content, in a non-transformative manner, no matter how harmless the intent is, if someone then uses it more maliciously in the future (like actually stealing and using it), those people could just refer to the first case where Nintendo didn't do anything, and thus make it a more difficult case for Nintendo to win.
It's probably not all there is to it, but I'd say it's at least 1 of the reasons. It's a reason that sucks, but a reason nontheless...