1/2 - 3/4" sand bed is all that's needed for nitrifying and denitrifying bacteria to flourish. Nitrifying and denitrifying bacteria actually exist in close proximity to each other (termed 'coupled') in the aerobic substrate layers with the denitrifying bacteria taking up residence in the sand grain's lower oxygen micro-pore environments. If you need more detailed info, take a look at 'The Reef Aquarium, Vol 3, pgs. 260-261' (Delbeek/Sprung)
Problems with denitification occur when advective flow into a substrate is impeded such as when heavy detrital deposits occur. The bacteria rely on flow to bring nutrients, especially carbon. With a decent amount of substrate that is regularly cleaned, as well as sufficient carbon and flow, nitrate should not rise to high levels even in a well stocked and fed reef tank.
Nitrate reduction from chronic high levels can take time, but just keep at it. Don't forget that most of the detritus will collect under the live rock due to advective processes, so it's a good practice to occasionally remove a base rock and vacuum under it (not always possible, I know).
Hope that helps...