It's not 1 company. Nintendo is merely the most visible and hands on. There are actual companies in the business of doing takedowns and lawsuits for less capable developers, and the stable of rights those companies represent grow all the time.
Anyways, reading your posts, I'm not sure you've read the official announcement on the takedown. If you haven't seen it, here:
https://www.emuparadise.me/emuparadise-changing.php