An emulator will be eventually created, it will simply display video as 2D or stereoscopic instead of displaying a paralax barrier image.
It's just a matter of re-arranging the slits displayed - it's not rocket science. I see nothing too complicated in this at all, Virtual Boy featured stereoscopic video output - 2 images, each directed to one eye, and an emulator was created anyways (using red/blue stereoscopy - 2 images that would normally be displayed separately were recoloured and merged into one screen, it's simple). The 3DS displays 1 image, it's just cut into thin pieces and arranged in a specific way. Re-arrange the slits and you'll get your "normal" image back. Read up on what a paralax barrier display is and perhaps you'll be less pesimistic.
The specs aren't really high, so I actually expect "proper" frame rates aswell.