Emulation might be legal, but it's software specifically designed to run illegal copies of the games.
I dislike Nintendo, but I can't blame them for taking down that kind of software development. They're still selling many of their old games through their own store for their own emulators. They're perhaps charging way too much for it and/or lock it behind a subscription wall, even if you ever bought the original copies. Absolute garbage business practice, but from the corporate point of view I can see why they go after emulators. Especially since it's easier to take those down than trying to go after all digital emulator copies of the games (if not impossible).
They're probably gonna try and set an example to scare off others trying to make new emulators too.
Edit: lol people really are shooting the messenger here.
Also, the amount of excuses that people have to make backups of their already purchased games is very weak. You damn well know that a vast majority of people don't use it for such reasons, the amount of people that still own original copies, and also have the hardware to even extract software for personal use must be like less than a percentage of the entire community using emulators. They're just people pirating games they never paid for. It's very naive to assume otherwise.