Nintendo's been plastering health/safety information in their systems since the Nintendo DS came out, but to see it to where it is inside of gameplay, that's a bit strange. I may not own a 3DS or even have held one before, but ever since the DS, every time the system even boots up, you're reminded to review the health/safety guide. The Wii says it twice: when you turn the system on, and before you play the game. (Some titles also have health advisements mid-game)
I mean, researchers have said that it's perfectly fine to have children less than six years of age playing (in fact, it's recommended to find vision defects early on), yet Nintendo says that parents should disable the 3D feature for young children. I'm guessing that Nintendo is just trying to be cautious, for there could always be one or two people that end up injuring themselves playing Ocarina of Time 3D or any other 3DS game...
(For the record, I've been replaying OoT and MM to compensate for my lack of OoT3D, and I must say, Tatl is definitely more annoying than Navi with her bell. >.<)