Well we don't quite know how a sonic shower works, as stated above... Maybe on the contrary is it much more efficient than a water shower, frying a lot of bacterias in the process (or vibrating them to death or something). On the other hand, a water shower could be much nicer to the skin.
I think they only had water showers in Enteprise; given that the NX-01 hadn't a lot of spare space, I suspect the water was replicated or recycled from somewhere. Therefore, water showers could be very easy to have onboard on starship, and I think sonic showers appeared only because they had an advantage over them (it being speed and efficiency).
"The main difference between Trekkies and Manchester United fans is that Trekkies never trashed a train carriage. So why are the Trekkies the social outcasts?"
Terry Pratchett