Before any of those people (you know exactly who you are) come into this thread... No. Nintendo cannot take down the GitHub repos that contain decompiled source code of the N64 Games that have been decompiled as this was clean-room engeneering and is completely useless without the assets needed for the game, and directly compiling the source code yourself or through a means like this PC Port. Classic Doom Source Ports have been operating like this for years, there's a reason why you need the original Doom/Doom 2 wad before you can mess with any mods even if the source code was directly released in that case.
I guess I'll be that guy.
For one, this isn't clean-room reverse engineering.
Clean-room is when one group (the dirty room) has access to the original product (in this case, Star Fox 64) and do whatever reverse engineering on it they like and then write up a detailed specification of exactly how the software operates, which passes through a legal team who vet whether anything in the notes is infringing before it gets to the clean room engineers who write a brand new piece of software to meet the specifications written by the dirty room.
The clean room never has any direct contact with the original product or any further communication with the dirty room due to the risk of becoming tainted with information they could not obtain without directly reverse-engineering the product themselves.
These decomp projects are
regular reverse-engineering, not clean-room. The same people doing the reverse-engineering are the ones writing the new code and they're explicitly comparing and contrasting their results against the original binary. Up to this point, none of what I'm saying equates to "This is illegal, you know," I'm literally just clarifying that this is not what clean-room reverse engineering is.
While clean room reverse engineering is undeniably legal, directly reverse engineering a product is at least
less clear. Under the DMCA, reverse-engineers are offered a narrow exemption when the work is done for the purpose of interoperability. This allows things like unlicensed accessory manufacturers for phones, consoles, etc. to exist, because without reverse-engineering how the original device works, they would be locked out of producing compatible devices or software.
You could make a fairly convincing argument that reverse engineering explicitly for the purpose of making ports like this is the most defensible form of reverse-engineered decomp, because they are using the information obtained to provide interoperability with other software than provided by the original publisher, such as the Windows operating system. It's less clear what protections a decomp produced for the sake of research, historical interest, etc. enjoys.
Ultimately, all of these laws are written with an implied assumption that these things are being done for commercial interest. Obviously, that's not the case here, it's just hobbyists doing things for fun, which isn't really a scenario the DMCA seems to have predicted. But I'd say there's an open argument to be made that a decompilation creates a derivative work of the original product, even if that decompilation doesn't do anything by itself (without game assets), because the program itself is a unique work that is part of a larger creative endeavor (the whole game). There's no requirement that a copyright violation has to be equally as functional as the original work in order to violate the original owner's rights.
Whether or not a decomp is a derivative work is something that simply has not been established in law, since previous shutdowns of similar projects have never made it to trial. That in itself is proof that companies
can and have taken down decompilation projects regardless of any argument as to their legality. You don't have to win a court case to shut down a decomp, just convince somebody shutting it down is a better idea than challenging a multi-billion dollar corporation.
The risk to these major corporations is that they take one of these cases to trial and lose, decomps are declared free and legal and it becomes open season; they can no longer use threats of legal action to shut these projects down unequivocally. That's a worse situation than the one they have now, where they can exploit the grey area to make whatever claims they like when threatening developers.
tl;dr: Nintendo probably
could take it down if they felt like it, not because they definitely have the legal right to but because it's a muddy, untested area of law and they have a lot of money.
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