Ah, the necessary room.
I have noticed their absence in many deckplans as well, deckplans are actually my speciality. My biggest problem as a planner is that I often include too many bathrooms, even on ships. Or at least what feels like too many to my sensibilities. The funny thing is when I ask women for input they say 'not enough' and when I ask men they say 'too many', which says a lot really when you think about it. I figure as long as they are both unsatisfied, I'm probably in the right 'ballpark' if you will forgive me.
One thing a lot of people miss when they do include bathrooms is that the bathrooms and other places of running water tend to be stacked upon one another. This is not always carved in stone, but it is so much easier to run the pipes that way you might want to consider it just from a designer perspective.
As to bathrooms in the pre-modern eras, it is my understanding that there were often places for public urination because of the use for the material itself (multiple agricultural uses, wool dying and even gunpowder in the later periods; lets not get into the teeth-whitening) rather than just using the streets. In fact there are times when the cry has gone out for urine collection in the aid of defense of the city, as in a bit of Confederate doggrel: "When a lady lifts her shift/She shoots a bloody Yankee...”
For mapping purposes however, the use of a restroom in some settings might not be that horrific a faux pas. I was doing a map for an Amber Diceless game once (Castle Amber herself) and suggested that tthere was a place for the restroom. The hue and cry went out, but given that Amber rests in the center of many different dimensions and has active trade with them, I think that a running water system would be one of the first things installed into the Castle. There might not be any gunpowder in Amber (before Corwin 'thoughtfully' brought it back) but the basic functions of fluid dynamics should work and at that oint its primarily a "would they have thought about that" sort of issue.
As for High Magic, I dunno. If they have lots of magic spread about like automatic quills and such, it probably isn't entirely out of whack. In that sort of setting, magic will be used in the important/viable places whenever possible, and having an indoor toilet is much better than a thundermug or a long ass trip in the cold and snowy season to the outhouse. It would get my vote before ever-inked quills.
The upshot is: I don't think it is something to always or necessarily be avoided in a pre-modern/fantasy style setting, but make darned certain that you have other examples of running water and the materials technology that is used in that process (tech for production and maintenance of the pipes themselves for example) present for that know-it-all that tells you it "wasn't possible". For myself however, I have grown tired of the complex explanations. Sometimes even though you did plan it out it is just something that is expected not to be there and no matter how reasonable some will simply not accept it. Nowadays I simply put the outhouse outside. I have done the same for some Post-Apocalyptic maps as well given that they understand the process, but the first time the systems break down they are probably not going to be able to fix it even if they know how. Unless of course they have plenty of parts and other equipment. Actually running water was the sign of prosperity in one of my Post-Apoc settings. They knew about indoor plumbing, many NPCs vocally lusted after it for the feeling of "normalcy" it gave, but it just wasn't always possible.