Its my understanding that a thin to none substrate is used to limit the amount of anerobic bacteria in the tank. From experience I know that ocasional stirring of the substrate can be dangerous because of the release of the "bad" anerobic bacteria. (bad bacteria has too much time in between stirrings and builds up in the substrate in alsrming numbers) Like some one else said if you have sand sifting type of fish that can keep it stirred up constantly then everything should be fine but if not be sure to watch your fish for a few days after tank is stirred up by vac and water changing. In a problem salt water system that we had I finally gave up and reduced substrate to 1/2'' and my fish started doing much better. Needless to say all of my own tanks are now limited to 1/2'' of substrate.