Id think they had some kind of other solution to the the waste problem than miles and miles of pipes through stone. Not that that is not possible, but obviously plenty of NEW dwellings have been built, and if so they would have no way of connecting them now with the old sewer systems, since the means of shaping the spirestone seems to be lost in history.
My guess is they have something that quickly dilute/converts the waste into something else. IE: you go in a pot, press a button and a kind of chemical solutions rushes in and combines with the waste and alters it into something less toxic (sand was mentioned, it could be broken down into water, etc.) Then whatever the byproduct is of the chemical reaction is either pure liquid and runs out through some (above the stone) pipes into large tanks to be collected for use, or if its solid, just gets collected once a day or every few days and thrown in the trash or a place to be recycled for further use.
Or, since this is steampunk, the waste is combined with a chemical to liquefy it completely, then a heating crystal evaporates it and the steam is pushed through some turbines to generate power or some other gadgetry before exiting the habble through the ventilation tunnels.