If the sand is too deep, and doesn't get disturbed enough then you will develop anerobic pockets. These will build up Nitrogen gas and if they get too big when they finally are disturbed the release of the gas into the water column could be toxic to your stock. A deep sand bed must be maintained in a very careful manner or else it is just a time bomb waiting to go off. Many people use MTS to keep the sand aerated to prevent this issue, but then you run the risk of a population explosion if you're not stocking anything that will eat them.