When you watch a 3D movie, your eyes are focusing just fine, they are focusing on the screen.
The human visual system conditions that are present in the movie theater are different that real life, since when you are focusing on the screen your eyes are verging in on objects that are not located in what is called the Zero Paralax Position, (ZPS) which is essentially the screen plane.
There is a zone of confort where the decoupling of vergence and focus is ok and there will not be any side effects.
This is achieved by not having too much stuff in negative paralax (in front of) or positive paralax (outside of) the screen.
Kid's human visual system is very adept. Filmakers are careful especially with kids movies to not have a lot of separation in the 3D especially since children's eyes are not as far apart as adults.
Finally most of these studies are old Japanese studies that were performed on old hardware and the results aren't really viable.
I've successfully decoupled my vergence and focus and you can too.
Also if you want to hear more about strabismus and 3-D look up "Stereo Sue" who actually had surgery to regain her strabismus and now is an avid 3-D fan.
This sounds like FUD to me