I do understand Nintendo being overly protective of it's IP, as Nintendo IS their IP. Without Mario, Zelda and Pokemon the company is nothing. Why would you buy a Wii U to NOT play first party games.
That being said, they to need to calm down and take a note from SEGA, or Star Wars or something, and let the fans show their affection. If you are not going to celibate Metroid's birthday, don't crash the fan's party (AM2R). There are probably better ways to protect your IP while letting fans create. I know there are 'protect it or loose it' clauses in copyright. If a company fails to protect their IP, it can be used against them, and weakens their ability too.
Especially when you take down something like the NP archive, yet you have no official upload of it all. Well, there are still ways of finding it. . .
Maybe Japan has stricter laws or something and killing all the fan projects is mandated from them.