In the secret room that you can access via a long crawlspace from the factory, where there is also a case with 10.000 skill points, there is a small toilet as well.
At the entrance of the secret Underground Lab under the Cathedral, there are a few cells where the doomed scientists and their equally doomed test subjects reside. Inside those cells, there are toilets that I don't think were used by the zombies.
There is a weird restroom in the Submarine. There is a toilet, a couch and a recreation table in the same room. Of course in a submarine the space is limited, and so are the options.
There is a row of showers close to the start of the Bridge section. This area is totally optional, as you can bypass it, but if you go through there, you will also see a J'avo under the running water of one of the showers.
In the cells where Jake and Sherry are held in China, there are small private toilets. Or rather, Sherry has a private toilet (it can be separated with a curtain), while Jake's is not private at all.