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VM Ware and Parallel are used specifically as learning-environmental tools for developers, schools,and engineers so legalities wouldn't be problem, concerning that said person(s)(companies) provide their own .iso. 

Emulators should be legal as they are a separate engine.  I have seen before though as others Nintendo taking down many of the ROMS featured on emulator sites and sites themselves, though there are still a few hidden that remain.

While it tickles me to see mod development like this (Homebrew,Emulators,etc) issues such as below have happened. Their corp/motto page also takes a firm opposite stand against emulators, roms, etc as snippet here: "

How Come Nintendo Does Not Take Steps Towards Legitimizing Nintendo Emulators?

Emulators developed to play illegally copied Nintendo software promote piracy. That's like asking why doesn't Nintendo legitimize piracy. It doesn't make any business sense. It's that simple and not open to debate."

http://www.businessinsider.com/a-history-of-fan-projects-that-nintendo-shut-down...

https://www.reddit.com/r/nintendo/comments/2o3bdv/all_roms_for_nintendo_consoles...

https://www.techdirt.com/articles/20141013/11010528810/nintendo-bricks-wii-u-con...

https://www.techradar.com/news/gaming/are-game-emulators-legal-1329264

While many players/fans are supportive of development, often times company is not. Personally, I think this development is great and opens up some nice VR opportunities.

Your post is a little confusing to me but i will try my best to answer you as directly as possible:

Nintendo didn't DCMA 3DNes because :

- Their lawyers know really well that they doesn't have the right to do it. 

- 3DNes  doesn't violate any Nintendo IP and is perfectly legal  

- Nintendo is just another company. It's not like that they are the representative of the justice, the law ,the court or something like that. We should only care what the law and the court says not what Nintendo think or say.

And FYI VMWare are vastly used in professional environment context.