i dont think they are actually rubber, more a plastic of some sorts. since the surface area is fairly small, i doubt it would offer much resistance really. if it was Saltwater id be more concerned, due to salt drying on the tracks, but with fresh i dont see it giving much of a problem.
i have a glass lid on my FW
but mine hinges in the middle. not had any PH problems from it but the back is open about 2inches and 2 HOB
filters offer a fair bit of gas exchange. the balas like to jump so i need a lid of some sorts, even then, scare them good enough, they can move the glass.. stupid things going to hurt themselves one day...
you know, lowes do sell small glass drill bits... many electronic stores, radio shack maybe, or even lowes, sell plastic nuts and bolts. you could hinge the glass using stainless steel hinges or plastic hinges of some sorts