Re: Hanging out in the litterbox?!
It is very common with shelter/rescue kitties. As you suspect, it's their safe haven in their little cage. Most do grow out of it, but I would make sure you provide another safe place for him. Even a cardboard box with a towel in it. If you find him sleeping in his litter box, take him to his new bed or box and put him in there. You could even put a little catnip in it for him.