I'm not so sure. It's possible Nintendo opted for a carrot rather than a stick in this case.

This doesn't seem to have been started with a public C&D letter like usual. Yuzu (the previous Switch emulator that was taken down) incorporated some proprietary Nintendo information, which is why Nintendo had a legal lever against them. They don't have one in this case, yet it still came down. Plus, everything seems to be have been going on very quiet behind the scenes.

If you were an emulator writer and Nintendo came and offered you life changing money in exchange for ending the project, would you take it? I would have a very hard time turning that down. Nintendo also doesn't want a flood of yokels trying to start the project up again hoping to receive the same offer; most would fail, but one or two might take off. Better to let the threat be implied.

This is just speculation, of course, but something about the way this has unfolded feels a little different.