Anaglyphic 3D gives me a headache if I use it for too long so I think you may be right that it is not great if used for too many hrs.
Stereoscopic 3D makes me feel a bit weird if I watchstuff for more than 3 or 4 hrs as well
...and jerking off to 3D pr0n causes more medical problems!
Couldn't resist saying that, but on-topic to Barth's point, he is right - hell even the 3DS comes with a medical warning.
Instead of me being a complete and total dick and a prick, I should be on my best behaviour!