no its not bad for your eyes. I read that its like excersing it hurts at first because your body isnt use to it. so do it very little a day in 3d. but eventually your eye muscles will adjust and actually become stronger. it also helps doctors find out quicker if u have an eye problem. if you cant see the 3d. they know your visual part of your brain messed up
It is not bad for your eyes, but if you have a smaller sibling about 6 years old or under, DON'T let them play your 3DS. If you don't like the idea of 3D anyway, you can ask a grown up to turn of the 3D for you (Parental Controls).