That's something I'd love to know, too! Our last cat did it his entire life. It's usually the kittens and young cats that do it at the shelter. Sometimes I think they get the urge to go while playing and just drop the toy while "taking care of business". They're apt to drown their toys in the water bowls, too.
I think the box is where their scent is the strongest and clearly marks their territory. Therefore he thinks the box is the safest place to store his toys.
If it bothers you, try to designate a new spot for his toys. It can be a cardboard box placed next to the litter box. Clearly mark the box by putting a towel with his scent in it. Once he gets it, you can slowly move the box away to an ideal spot.