I downloaded and converted a video of the Wario Land game in 3D and played it on my 3DS. People's worry about eyestrain are unwarranted. Think about it though, why did the Virtual Boy hurt people's eyes? It used shutter glasses, like the ones in most 3D TVs but much slower, so there was a constant flickering. That, combined with the colour pallet, was what hurt your eyes.
If they did it on the 3DS the problem wouldn't be there