Coming from an Eye specialists speaking to the New York Times:

“The fact you’d watch 3-D in a theater or a video game should have zero deleterious impact whatsoever,” – Dr. Lawrence Tychsen, a professor of pediatrics and ophthalmology at Washington University in St. Louis.

“I don’t think that parents need to worry about kids playing video games, 3-D or otherwise, from a vision perspective. The bigger question for parents is: Do you really want your 3-year-old playing a video game?” – Dr. David Granet, a pediatric ophthalmologist at the University of California at San Diego

I am not a specialists on eyes, but no one can say for sure what the full effect 3D will have on the human eye. The longest 3D experience I had was for Avatar; what two and a half hours?  Has someone really sat down and used 3D like a six year old would, play games 4-6 hours a day, day after day? We can not say for sure how long exposure to 3D can affect our eyes. Nintendo is covering themselves just in-case there is an effect on the eyes.