Our bridge crew simply has such waste products beamed away to be recycled on a subatomic level whenever sensor readings on them detect that it is needed. No fuss, no muss, and it extends to the rest of the crew if we're at Condition Yellow or Red. Not that it is an issue for yours truly at all.
Sonic showers are just silly, too. I mean, sure, that might have been necessary back before the 24th century, but we can pretty much effectively replicate and unlimited water at whatever temperature desired. Unlimited enough for the crew to shower all they want, anyway.