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As a guess, Nintendo is issuing this warning because there is (probably) a small chance of irreversible harm being done to young children's eyes with excessive use of the 3DS; and by making announcements, and repeatedly stating that the 3DS should not be played in 3D mode by children under 6, Nintendo limits their risk to potential lawsuits.

With that said, I don't really see this as much of a problem for Nintendo because most children won't get a device like this until they're 8 (or older); and Nintendo could potentially have an option in parental controls to disable 3D mode.