It'll definitely become a problem for Nintendo, but it's not something damning for them. Hacking and piracy eventually becomes a thing in most gaming devices, like the DS, the Wii, and the PSP, which I recall being a particular issue with (My friend bought a PSP just for the modding). It's problematic and annoying, but it's nothing new at this point.
Dance my pretties!
The Official Art Thread - The Official Manga Thread - The Official Starbound Thread