I'm actually really worried about how the 3DS would effect my eyes. I have an eye condition that gets progressively worse which will most likely require eyes surgery sometime soon (not LASIK but real cut your eye open and poke around type surgery), so I'm pretty apprehensive to go near a 3DS.
But given the way the 3D works on the 3DS, it will affect some people more than others. There are some with a condition that cannot process 3D well and actually get sick/headaches. Its actually the same with 3D movies.