Nintendo is well-known for using emulation in its own products, such as “Virtual Console” releases and the “NES/SNES Classic”. They just don’t like people playing their games in ways they didn’t decide on.
Emulator projects should all add a clause in their EULA that specifically forbids Nintendo from using their software, then they can sue Nintendo for breaching their license. Give them a taste of their own medicine.
I personally don't think it's so likely that Nintendo would write and maintain a Windows emulator just for their museum if an open-source project exists that they could legally use for free under that project's license terms. Only someone with insider knowledge would be able to say for sure though.
That's fine and all. I agree that their actions are absurd. But the aim of this article seems to be to provoke more rage towards Nintendo for something that seems like pretty standard practice and completely misses the point of what people are mad about.