the last step of the nitrogen cycle is the one that a deep sand bed will perform. chaeto will also get rid of nitrates. the live rock in your tank and the shallow sand bed do little nitrate to nitrogen conversion, so without a way of exporting the nitrates (like macroalgae) you may get a small buildup of nitrates. the reason a deep sand bed gets rid of them and a shallow one deosnt is, the deep sand bed allows for an anoxic zone for facultative bacteria to change nitrate to nitrogen. a shallow sand bed does not have an anoxic zone, so those same facultative bacteria will not change nitrate to nitrogen.