Well, the vision of babies and very little children is developing. Even 3D or sharpness must be learned. As the artificial 3D is generated differently it might lead to the childs learning wrong to look. But thats for very little children.
Nintendo itself cautiosly recommends not to use 3D for children aged six or under. Above that it is safe.
https://www.nintendo.co.uk/Support/Nintendo-3DS-2DS/FAQ/Safety/For-which-age-ranges-is-the-Nintendo-3DS-system-recommended-/For-which-age-ranges-is-the-Nintendo-3DS-system-recommended--244139.html