Like everyone said, neutering would certainly help. Maybe he is spraying urine and you didn't notice.
The chances of him dying during the operation are pretty slight, especially considering your rabbit is young. There are around 0.3% of rabbits dying during this procedure, and females are more at risk, older rabbits too and the majority of the rabbits dying is caused by heart problems that the rabbit already had or allergy to the anesthesia. So, don't worry too much about the risks. The important thing is to have a vet who has experience dealing with rabbits (I'm not above asking a vet if they do that kind of procedure often or if they think I should make the rabbit fast before the operation to check if they know what they are talking about and please, ask something for the pain, like Metacam, after the operation if the vet doesn't give it to you).
About your current situation, do your rabbit have a litter box inside his cage or do you put litter all over it? How often do you clean it up? If you don't have a litterbox, I would advise you buy one and train your rabbit to do his business there as it is a lot easier to clean, it smells less and it is better for the rabbit who can enjoy the clean parts of his cage. It is a LOT easier to train your rabbit to use the litterbox once he is neutered.
Also, the litter is sometimes at fault in odor matters. I once tried corn and it was awful - it smelled something awful. What are you using?