The reason the skimmer works better in deeper water is that there is less "head" pressure on the pump. The pump is pushing water into the skimmer, and the more distance between the water level in the sump and in the skimmer, the harder the pump is working to maintain the water level in the skimmer. Since it's working harder in shallower water, the water speed through the venturi is a little slower and less air is drawn in. This is the nice thing about recirculating skimmers, they take the 'head" pressure out of the equation.