A filter will not cause a nitrate problem. If you use a mesh media it will have to be cleaned often. But if you only use carbon or something simular you would change as needed, but you would not have to clean the hole filter every time you change media. If you cleaned or removed the filter the bacteria would just grow elsewhere in the system. Bacterial populations will fluctuate based on the nutients going in the system, where they grow in your system is irrelevant. Nitrate problems are usually caused by heavy bio-load and or over feeding. You have to have a balance between the nutrients going in your tank(food of various types) and the nutrients coming out(via a DSB, plenium, refugium, algae scrubber, water changes, skimmers, etc..). When you have more going in than coming out you get excess nitrates and it has nothing to do with filters, bio-balls or any other surface where bacteria will grow.