I would venture a guess that your concern, or feeling of need to clean the bottom of the tank stems from the fact that these fish are big eaters, thus big eliminators. Clown loaches need pristine conditions to do well.
Another reason to have a really big tank, with extra filtration.
How often do you do water changes, and how do you do it? Do you just take water from the tank and replace it, or really get in there with a hose and get the detritus up off the bottom? What kind of substrate does the tank have?