For example the Ship of Harkinian PC port of Ocarina of Time. This requires a legal or illegal copy of the original game to run, so the copyright authorities don't crack down on it yet.
Are we sure that this is the reason the authorities aren't cracking down on it, and not that a game released in 1998 that also has a newer release on the 3DS just isn't financially valuable enough at this point to try to protect now? And it's getting an even newer remake, which is where Nintendo's concerns would be, I'd assume.
Yes, because Nintendo is constantly taking down projects that cross the unspoken line and redistribute assets.
Nobody can be sure, but there is a consistent pattern here: decompilation projects can include as much code as they want and not get punished, but if they include assets they are taken down.
I suspect it's actually because the authorities don't know what the project is, if it's only code, or they can't be sure it's an infringing derivative work (it is).