Actually, emulating a 3DS should be relatively easy. In addition to just being a lot slower than a Wii U there's also the fact that both the 3DS and Switch are ARM-based so you don't need process-level emulation in the first place.
But there are obviously more practical, UI issues like how are you going to play a 3DS game with one screen and no touch...
Well a single screen shouldn't be too much of a problem, just dedicate half of it to one output and the other half to the other output. The question is just whether it is better to put them side by side (ruining the effect some games tried to have by treating the two screens as one long display), force the player to turn the screen to play 3DS games, or just have a lot of unused screen space. None of those are really good solutions, but they are workable.
No touch screen however would be an annoying issue to work around. Honestly that hadn't even occurred to me until you pointed it out as I just took it for granted that the NS would have it since that has been Nintendo's thing for so long. They could probably make their emulator have a cursor that acts as the touch screen, but that doesn't seem like a good solution unfortunately.