How many shrimp do you have in your tank and how large is your tank? Do you use a sponge on the HOB and if so, have you tried turning it up so it circulates to the bottom. Where is the filter placed? I would put it in the middle of tank if possible.
You also might can save yourself some stress to either sale some off or transfer some to a new tank so you don't have so much buildup to stare at on the bottom. I will say having some substrate will help here if and when you may use it. But my coffee filter/hose method works for water changes alone. Its not going to take care of the bottom.
