Doubt it. Microsoft could face a hefty lawsuit from Nintendo if they didn't actively try to stop these emulators from getting on the system through their distribution channels.

There is nothing in the system that prevents an app like an emulator to be published, it's accepted according to the guidelines by MS.

But yes, it will be removed, most likely.

Also there are ways to avoid an removal also, for example if someone would publish an app that is intended for reading news, but a small feature of the app allows for NES emulation. Just as an example. This would be much more difficult to get removed, because the intent of the app is not to be used as an emulator.

They won't remain on the Xbox one as apps why exactly? Surely not because of Nintendo. They are currently available on any android phone tablet and gaming console through Google Play store, windows phone, Windows 8 PC and Tablet through Windows app store and iTunes.

If anything Microsoft will remove them as they are greedy evil bastards and don't want you to enjoy your $499 console with free retro games.

Those guidelines will probably be updated for universal apps. It's a gray area and Microsoft didn't fight against emulators on their system they'd just be asking for Nintendo to sue them.

Yes you are right here. There are updates every month for the guidelines so it could change very fast.

Does that mean SNES and GBA are doomed?