It's similar to seat rows in the cabin without windows.

Aircraft manufacturers lay the aircraft out with windows where they think reasonable. Deleted windows are generally due to cable ducts etc passing behind the wall.

Airlines then all do their own thing with interiors, which are also changed round over time, and for some the layouts end up with windows alongside where they wish to put toilets. It really is quite a way down the list of priorities, if there is a window there so be it.

Time was that operators would delete windows with metal blanking plates known as "plugs" where they were not required, they were usually quite obvious under the paint scheme. As aircraft structures have got more sophisticated this approach has lost favour.

The BAe 748, at least, had not just a window but an emergency exit out of the toilet compartment at rear right of the aircraft in the typical layout (certainly BA's were this way). To use the exit, squeeze past the facility.