The Enterprise D bridge toilet is supposed to be in the same 'alcove' of the Observation Lounge door. To its left as you look at the bridge from the front. One would assume people have toilets in their quarters too. I honestly can't think of too many non-Trek programmes that make a point of explicitly stating where the jacks are in any case.
And we do see the sonic shower in Voyager and the non-sonic one in Enterprise.
The reason we seldom see bathroom facilities featured in Trek is because most of the time, it's not relevant to the overall plot. Exceptions include Janeway in the bath when Q pops by, or when the Doctor intrudes on B'Elanna in the sonic shower.
Further details and examples can be found under Live Action TV > Star Trek of:
I also think though not positive that showers have been shown.
Showers have been showed in ENT, there was an episode where the artificial gravity went off-line when capt. Archer was in the shower.
And there where showers in various other ENT episodes.
And there was an ENT episode where children where asking the crew questions and one of the questions was: "When you flush the toilet, where does it go?"
But I can't remember seeing a toilet in the show.