I believe the legal issue is that there has to be specific headers (?) in a rom to run on GBA, and Nintendo copyrights those headers and the data in them. So anyone using those without Nintendo's permission is breaking the law, and Nintendo won't give permission to games that aren't approved and aren't manufactured by them personally. That said, if a hobby developer were able to get a game to run without any code from Nintendo (which I believe is possible), I don't think it would be illegal to then distribute that game. Might piss Nintendo off, but I know the fact that devs have to use a little bit of Nintendo code is how they legally force everyone to go through them. Lots of publishers released games on carts in the 2600 and NES age without permission from Nintendo and Atari. Since then, it never occurs.
I'd have to ask my coder pals for clarification, but it's something close to this.
