Snakes use Urates instead of urea like other animals because it takes less water to flush the nitrogenous waste out of the body. It is comprised of a high percentage of uric acid. I have read that it breaks down much more slowly than standard urea does, and could therefore be not as harmful to plants. But, in such a closed system, I'm not sure if you would want to leave it in there and risk it. You could always bury one and see how it does over some time. If it is a bioactive setup, does your cleanup crew not touch the urates?
Personally, I would spot clean the urates. Have you checked with other people with a bioactive setup to see what they do?