...But if the latrine is just a latrine, and is included only for the sake of realism (you DID measure rise over run to make sure the pipes would drain correctly, didn't you?) then many of us don't really care whether or not it's there. Maybe, for some people, its absence would be a glaring inconsistency, but I think being bothered by things like that is a choice.
You're missing my point. It isn't all times you make sense that drive the story as a notable event- it is the things that do not make sense. Seeing a latrine is not a magical experience that makes the game better. Dropping in the latrines, and the sleeping quarters isn't going to (often) be the payoff. It is the setup for the payoff.
Let's say you're playing a game in which there has been a waste disposal option for creatures everywhere you go. Sometimes it is just a deadend corridor. Sometimes it is a portable hole. Maybe an Otyugh. Maybe some oozes. Sometimes it is a river. Whatever - but the DM made sure there was an option for waste removal.
And then the PCs come to an orc cavern system and discover there is no waste removal option. This is a potential clue the PCs could note to indicate that maybe there is more to the complex than they've found. Maybe the druid wildshapes into an animal with a good nose and follows the faint smell of waste to a secret door. Maybe they just say, "they have to poop somewhere" and search the caves again. Maybe they speak with dead and ask where the orcs pooped before they died (and if you've never experienced the grand magnificence of Post Mortem Excretion Interrogation I feel sorry for you). But it can be a trigger for the PCs to figure something out.
And I promise you, players - across the board - love to feel like they figured something out. Not the PCs. The players. Even if they have their PC blindly stumble into the trap because the player realized it was thre and the PC didn't, they love to feel like they solved the puzzle you put out there.
Now, a DM could 100% just tell the players, "You don't see a latrine option. You think there must be more to the cave," That can, and does, happen in games. However, that type of dump of answers to players is a weak way to move the game forward. It takes agency away from the players. Even if you gatekeep it behind an investigation role, you're just reducing the game to dice rolls and DM dictums. The more tools you give the players to identify and apply, the more options they have to feel awesome.
There is, of course, middle ground as well. There are a lot of DM styles. However, I'm not talking about the spectrum of ground - I'm talking about the things you find when you venture to the realm of making settings where the dungeon makes sense. All I am, and have been, saying is that making a sensical world where you can apply 'real world' logic and figure out clues based upon the logical conclusions gives a DM stronger and more immersive toolset to create a game where players get to be more involved. I am not telling you that you have to play that way - just that if you do, it gives you tools that can be really rewarding.