Please email me at Sales (at) TunzeUSA.com so I can send out some replacement silicon pads for you. They are there largely to prevent scratching, but also help with noise reduction.
Great observation about the lack of a rubber gasket. There is actually a gasket, of sorts, but it's a gasket made of water. The way the water is routed in the skimmer body creates a boundary layer of water around the entrance to the reaction chamber. (The reaction chamber is the lower section of the collection cup. They're integrated to make cleaning easier.) This boundary layer keeps the stream of bubbles focused towards the center of the reaction chamber. We use the same water gasket method on most all of our skimmers, from the DOC Skimmer 9006 to the DOC Skimmer 9410 all the way up to our largest, the Master DOC 9480.