I would not put it past Nintendo if they start targeting here though.
This is very unlikely to happen. For various reasons.
This is Nintendo we're talking about...I would not be surprised if they try to destroy fan translation too.
That is equally unlikely.
1. Modifying game code is legal as is the patches and utilities that provide such. Otherwise cheat devices and codes[such as Game Genie, Action Replay, Codebreaker and the like] would similarly be unlawful.
2. Most of what is hosted on RHDN is falls under the umbrella of "fair-use". The instances that do not are hosted with the permission of the creator.
3. RHDN is not hosting the games themselves, only patches that can be applied to them.
4. RHDN is hosted in Italy. Italy is well known for having a very different stance on copyrights. The DMCA is not upheld there generally speaking.
5. RHDN is not profiting or gaining revenue hosting said modding content. It is completely non-profit IFAIPK.
6. RHDN actively promotes the educational side of modding/hacking/translating.
RHDN being shut down? It's possible, but not for the reasons discussed here.