Pits are scarce enough in this game that I don't think it would take all that much more design effort to eliminate them entirely. It's not that they're really a problem, only that the Sonic 3 level design formula encourages checking out every little nook and cranny and consequently it's jarring when you do that and there's just nothing there. If it's supposed to be lethal, line it with hazards. If it's a case like Flying Battery where there obviously shouldn't be anything off the bottom, at least go the Sky Sanctuary route and pad the lower edge with wind.