I agree with mojoreef. I siphon my bare-bottom sump chamber once a month to remove any built-up organics and mulm that gather there. What you are seeing is the debris settling out of the water column, much like it does in your tank. Biggest difference here is you don't have a substrate to hide the waste
By siphoning it carefully, you shouldn't hurt any of the existing (scypha) sponges you have. Talking from experience here.
-HTH-
Cos