What size grain is your sand bed? The grain size greatly affects the required depth for creating a deep sand bed. 4" is the bare minimum using sugar/fine sand, but it will work. As far as denitrification goes, if you do have a viable deep sand bed, you don't need any more rock. In fact you probably couldn't cram enough rock in there to outdo a deep sand bed without removing all space for your fish.
If you have not already done so, remove all the sponges, floss, etc from the HOB filters. They're really only good for carbon media and cheap, gentle circulation. If you still have the physical filters in the HOB filter, this is likely your source of nitrates.
