Wait are we arguing that the owner of something isn't entitled more than someone who bought it?

FTFY. The problem is not with Nintendo being against emulators because of piracy, they're against emulators even if you own the game and the hardware but want to preserve the hardware (just like they do in the museum).

And if the counter-argument is that you don't own the game when you buy it, then by that same logic you don't steal it when you pirate it.