Welcome to nutritional science. This is common with just about everything in it.
When I had to take a course on it, this was quickly pointed out by the professor, with an egg as the example. Some years it’s the best thing you can eat, others it’s the worst.
Because emulation is legal. It shouldn’t have to be hidden. This was taken through the courts in 2001 with the Sony vs Bleem lawsuit.
What appears to be happening is Nintendo is abusing its power and money to make threats of legal action that these groups just can’t afford to fight, even though they haven’t done anything illegal. It should be coming as a surprise that Nintendo is coming for them, because this is completely legal, and not some fan game using Nintendo IP (which is what they normally shut down).