I'm no scientist, and I am not that experienced with this whole reef thing. However, I've had two tanks now both of which had diamond head gobies in it and after observing them and observing the tanks I find it highly unlikely that they "kill" the sand bed. The reason I say this is that the sand beds of both my previous aquarium and my current aquarium contained a lot of worms and and little critters, additionally when I watch the little bugger eat there are very large grains of sand that go through his mouth and come out below his gills, it seems unlikely to me that the filter in that fishes gills is efficient enough to completely clean out the sand that he's sifting through. Maybe it's because my gobies have been small, and I most certainly could be wrong but it just seems a bit unlikely to me.
Lots of critters also live in the sand and rock. So if you've got lots of rock, the sand will be repopulated to some degree from your rock.
If I shine a light into my rock any time of day, I see pods scurrying around like crazy. The more nook/crannies/holes, the more pods!