They do have 1/2, 3/4, and 4/5 scale guitars. Most 9-year-olds might benefit from at least a 3/4 scale guitar. My 5-year-old has a 3/4 scale Squire Affinity Strat, which is electric. Which guitar should depend on what type of music he wants to play.
Many people recommend learning on a 3/4 scale nylon-string guitar because it is easier on the fingers, but if he is trying to learn System of a Down, for example, it won't be of much benefit to get an acoustic.
I will also say something about which I feel strongly. Learning an instrument is difficult enough without having to battle with it. Make sure you get a guitar with decent action. As I understand it, many people give up playing guitar because of the instrument itself. If the action is bad, or some such thing, the player has trouble determining whether the "bad sound" derives from his ability to play or the guitar itself.
That being said, I got my son his guitar from Musician s Friend.com
. It was $99, and plays fairly well. I would recommend peeking around that site anyway. They have sections for student guitars and less-than-full-scale guitars and accessories.
Good luck. Let me know how the story ends.