Leaving the fecal matter to decay will raise nutrient levels in the aquarium water. However, the increase is presumably very minimal. Invertebrate fecal matter is not usually cited as a major contributor of nutrients. In fact, I have heard that one reefer had to switch from ghost feeding to ammonia dosing while cycling their tank when the hitchhikers on their live rock ate the fish flakes they were feeding, preventing ammonia levels from rising.