Not a Wario fan, but I have to admit that was a cool game (I played a store demo of Wario on VB).
Creating 2D from 3D is a simple matter of showing only one of the two camera angles. That's how the 3DS handles 2D mode for video and photos (repositioning objects for a dedicated 2D angle is not possible in either case). There's no reason that cannot be done with a simple emulator tweak. Granted, Virtual Boy was never MEANT to have a 2D mode, so it's certainly possible some games will suffer for it. But technology-wise, there's no reason it cannot be done.
While it is Nintendo's policy that all 3DS software must have a 2D mode, how exactly the 3DS responds to the 3D slider is up to the software being played. As mentioned above there are instances where it is necessary to be a simple on/off switch with no analogue functionality; Virtual Boy could easily do the same. Going the opposite way, Excitebike does more than just intensify the depth, and actually has the camera pan to a wider angle as the 3D effect is raised.
Also on DeviantArt, Rumble, DLive.tv, and the Fediverse (@freespeechextremist.com and @bae.st)