I read through it and the only thing I could find about JR/YR, particularly speaking of rider/horse combinations is this:
18. Championship classes for juniors and young riders and Dressage Seat Medal Semi-Finals classes must only be held on weekends, including Friday. Juniors and young riders’ entries (horse/rider combinations) are limited to entry in only two championship classes, excluding freestyle.
I read the above to mean that you can only enter 2 classes (i.e. 2nd and 3rd). Nowhere did I find it stating that you could or could not ride 2 horses in the same class. As long as you qualified on both horses - you should be able to ride them.
Yep - riders may ride as many horses as they can qualify . You can only ride one division per horse (so you can't ride the same horse in both the open and Jr/YR championship classes).
A horse, however, can only be ridden by one rider at the championship show (so, for instance, trainer and client can't both show at the GAIGs if the horse is entered in a championship class, even if the horse qualified with both riders).
Edited to add: see point C-13 on rprincess' link : 13. There is no limit on the number of horses on which a rider may qualify.