Looking through the source, there doesn’t appear to be anything the Big N can do to shut this project down. This isn’t like a ROM hack or an actual “fan game”, it’s using the decomp, which the Big N has no say over
I'm not a lawyer and this isn't legal advice, but I'm not so sure that the decomp itself is entirely safe from the ninja treatment. The upstream decomp (and, in turn, this port) contains assets ripped directly from the original game. For example,
this Lapras sprite, as well as every other sprite that the game uses.
Putting aside for a moment any moral arguments about copyright enforcement, those sprites are Nintendo, TPC, and Game Freak's intellectual property. Technically even including the likeness of one of the game's original characters in the repo would risk violating copyright law in the US. Including the original artwork from the game, in full, only serves to increase that hazard.
Now, does that mean that Big N knows about this, cares enough to do anything, or wants to risk the backlash that may accompany doing so? That's unclear, and only they can know that. Regardless though, I think a lot of people have some serious misconceptions about what constitutes a "safe" decomp project.
To properly safeguard against copyright law enforcement, you need to make use of a bring-your-own-ROM system and extract the game's resources from that while compiling/packing the output binary.
Ghostship does a great job of doing that for SM64, for example, although I'm not sure if they extract the less obviously copyrighted assets like dialog strings alongside model geometry, etc. That's also (by my understanding) why ROM hack patches are generally safe, since your patch file doesn't technically contain any identifiable intellectual property without the source material to patch against.
Source
