Seems like the sort of thing that Nintendo will want to shut down. There are legal loopholes that can be taken to avoid copyright infringement in such cases (such as releasing a game engine without any reasources/assets a la the Super Mario 64 decompilation project), but it doesn't look like this SM64-on-GBA project is doing anything like that. (Which is unfortunate. Other projects like the Link's Awakening PC port that got shut down not too terribly long ago also didn't take precautions.
Don't get me wrong. I hope this project sees the light of day. I just don't think Nintendo will let it. And I wish the creators of these sorts of projects would take the necessary precautions to avoid being shut down on copyright grounds.