Unneutered males have stinky urine just by itself. This can be compounded if they are also spraying urine. You might be cleaning the litterbox everyday, but if there is urine on the walls or floor that you don’t see, that will permeate the house. So males really should be neutered if they are kept indoors.
Unspayed females may be stinky, or they may not. Females can also spray urine, and there is an increased chance of urine accidents if they are not fixed. Just like with males, you may not notice the accident, and it may begin to smell. And of course, females MUST BE spayed due to the high risk of uterine cancer.
A spay/neutered rabbit that has his/her area and litterbox cleaned out FREQUENTLY really should not have any offensive odor. There will be the smell of hay, and possibly wood if you use wood stove pellets for litter, but most of us don’t consider hay and wood smells offensive.