I don't think that Nintendo's warnings are completely void of scientific evidence. I remembered something from my Psych class that I just looked up. Child good Development Stages.
http://en.wikipedia.org/wiki/Child_development_stages
The idea that I gathered was that as we grow up, we have critical stages for different functions like hearing and vision to develop. There are different case studies like cats that had trouble interpreting vertical lines after growing up with these sort of binoculars that only let horizontal lines through. The theory is that if we never get the chance to develop these certain functions at the right time in our life, we could severely damage the future development of that function.
Nintendo's reasoning might be that the 3d isn't a natural thing for the human eyes to look at. It simulates 3d in real life, but it's not 3d. For a child that is starting to develop vision and Binocular cues(which the wikipedia article says become well developed at age 5), it wouldn't be a stretch to consider the implications of having a child of that age constantly staring into a simulated 3d environment.
I don't think it can be compared to simulated audio on earphones. Looking out onto a landscape is completely different than looking into your 3ds screen. Listening to music on your earphones isn't that different from sound coming from your environment in comparison.