I'd love it if Emulators added a license clause forbidding Nintendo and Nintendo affiliates from using it then took them to court.
I understand your concern. But (assuming you're talking about FLOSS emulators) if they added that clause in the license, it would cease to be free and open source.
One of the basic properites of Free Software is freedom 0: the freedom to run the program as you wish, for any purpose. Even for purposes that you don't like or disagree with.
The thing about open source is, you can't grant those rights selectively. It's gotta be for all or none.
The article dosen't say what emulator they're using, but I seem to remember reading something somewhere that Nintendo has their own internally developed emulators for for running on PC