this is actually a pertinent question for me as well,Stewie is intact and he has very skunky pee, he's old enough now that he could get it done safely if i can find a good rabbit savy vet in the area, the problem is they are all cat and dog only vets!
he has a litterbox that he uses and i use aspen bedding as litter but it isn't doing anything for the smell, and i don't remember Howie's pee smelling so bad