You know, honestly, I agree that there should have been SOME kind of facilities written into the game. Not that they need to function. Not that there needs to be a /takedump emote The fact that they AREN'T there isn't the end of the world to me, but it WOULD soothe my sense of "completeness". There are LOTS of games that I can think of that have a toilet built into them and its not a big deal. List follows:
Goldeneye64 - If i recall correctly, one of the missions STARTS in the public bathroom, after dropping out of a venitlation shaft. And i think there was a conveniently forgotten handgun lying around in there too.
Harvest Moon: A Wonderful Life - There's two little rooms off the kitchen... you can't see into them, but take your little player in one and you hear a suggestive little *bloop* followed by a sigh of relief. Hilarious!!
Animal Crossing - There isn't a bathroom per se, but you can get a toilet as one of you pieces of furniture in the house, and you can sit on it (feet dangling and swinging like a little kid too hah!) and flush it.
Mass Effect 2 - There is both a men's and women's head on the Normandy (spaceship) and depending on the gender of your character, you will only be allowed by the ship's AI to enter the right one

It also has a bedroom (for *ahem* well nevermind) and a kitchen (though I don't recall if you actually EAT there... just talk to the cook who is also the ship's janitor...)
I'm sure there's more, but I don't want to take up all your time. All that being said, I know that retro-programming a toilet space into the older games is a bit much to ask. And trying to insert a toilet space into Uru as it is right now might be a bit much too. And until there's a day when new Myst-universe games are being developed (which I'm afraid will probably be never), I suppose we'll just have to cross our legs and hope to die.