I remember when I was in grad school 10 years ago the experimental 3D systems would give me horrible headaches after a few hours of use. I remember thinking that if we shipped 3D systems like those to average consumers it would be a disaster. Other grad students reported vertigo and one even vomited after an extended session.
The saving grace of these systems might be that they aren't fully immersive so you would avoid the vertigo we felt standing inside the CAVE. The headaches came from the shutter systems we used. I'm glad 3D in theaters today uses some sort of polarized light these are much more pleasant to look at.
I think as long as 3D remains a "treat" instead of a default experience we'll be okay. The fact remains that no matter what the system used to produce 3D illusions on 2D surfaces we are ultimately causing a pair of binocular eyes to see objects that are not there. Seeing things that aren't there just sounds bad for you.