Nintendo hates emulation that isn't generating Nintendo revenue, to be specific. They sell emulator hardware and emulator software via their platforms.
They would make more money from emulated content if they allowed you to transfer your purchases to the next generation console.
So they don't just want to make money off of it, they want every emulated Nintendo title to survive the same way Grand Theft Auto or Skyrim does, except it's just you buying it over and over again on the newest Nintendo console.
They don't even let you buy MOST old games to emulate officially. There's plenty of SNES, GBA, etc games that do not have a legal path to play other than finding the original cartridge on ebay and hoping your original hardware still works.
And then they're spotty about what they'll actually allow you to buy that way anyway. I would have loved to play the first NA released Fire Emblem legitimately, but they only released it for WiiU.
No one stops them from selling DRM-free images of their games to be run with any emulator on any platform and generate revenue from that. They don't, so it's their own loss pirates provide that flexibility instead.
