If you are not running a DSB in your display, then i believe that siphoning of the substrate is crucial in the elimination of nitrates.
I believe that there will not be too many pods in your display substrate, they would more than likely be hiding in your live rock in the dark. Your fish would grazed any pods creeping around your substrate.
Using one of the gravel cleaners that you can find at the LFS (the one with the long tube) is ideal for syphoning. Because you can plunge it into the gravel to get all the crap deep in the substrate, you eliminate dead spots in the substrate that could be harbouring toxic gasses.
I used to siphon the top 4-5 cm of my DSB where I could reach and experienced no negatives from doing this. The waste wtaer coming off thsi was soemtiems choclolate brown - thsi in atank that was fed EXTREMELY lightly, and with a lowish fish bioload.
But my DSB was in the main display and only siphoned maybe 25% of it at any time (could not reach the rest), so it's size was more than capable of picking up any slack from any portion of the DSB that was damaged by the siphoning.
On a smaller DSB (relative to tank water volume, I would perhaps be a bit more cautious. Since I removed my DSB from the main display and moved it to my sump (now about 20% size of my original, I have not siphoned it at all, but I do try siphon all the gunk form my bare bottom main display now.
I do think it is important to remove as much detritus as possible, whether or not that detritus is in a DSB or SSB. The thing to note is not to disturb the DSB too much if at all possible (try do the surface only), failing that only do a portion of the DSB at a time to allow critters etc. time to migrate to newly cleaned areas, before tackling another area.