As for how "clean" emulation is... let's be honest here and put potential piracy related issues aside, Nintendo aren't funding and making these exclusives just so that you play them on your PC.
A huge part of the reason why they fund these first party titles is to make us, gamers, buy the hardware. If that wasn't the case, we'd have Nintendo games officially released on PC and other platforms. Personally, I think it hurts Nintendo's business to emulate their games if it's stopping you from buying the hardware.
To illustrate this point further, I doubt SONY funded Bloodborne development with the sole intent of selling just the game, they want me to buy a PS4 as well. Another example that I have to mention is the Halo franchise, Halo games are made exclusively to the Xbox, despite the fact that MS would've benefited regardless of what platform you choose to play the game on, they wanted you to buy Xbox consoles so they can expand the userbase.
One can make the case that emulating first party games and third-party games funded by hardware manufactures isn't the "right thing to do", and I wouldn't disagree.
