Here's the thing...the die hard pirates, or the techno geeks that get more of a thrill out of emulating it than owning the real hardware and playing it...for the most part, these are NOT Nintendo's customers, and never would be under any circumstances, regardless whether there is a working emu or not. There are more of these people on forums like this one for obvious reasons, but are such a minute fraction of the game playing market that it's not really a big deal.
I could pirate a lot of games, but if I am very motivated and interested in supporting a company or game series then I am going to buy that game as my vote to encourage more of the same. In fact I collect zelda games, I own quite a few of them.
Now, if/when the pc version has superior aspects like graphics, save states or such, it might be cool to run it that way. I'd have no problem with people buying the game and then running it on their computer. If you like zelda and want more I encourage everyone to buy it. If you don't really like it and are indifferent, wouldn't ever buy it even if you couldn't play it free, then honestly you aren't going to help or hurt nintendo one way or the other even if you pirate it.