As someone who uses yuzu to play games at 4k, I have bought 2 switches and purchased the grand majority of the games that I have played on emulator. While I think it's true that devs lose some customers this way, most people who are playing BOTW on their pc (requiring a pretty good computer) pay more money into the nintendo ecosystem than many people imagine.
If anything the way nintendo treats it's competitive communities makes me feel bad for giving them too much money. But on the other hand they are one of the only devs who consistently ships quality finished games, so that should be rewarded.