In Duke Nukem 3D you could take a crap in the bathroom, and that game is from 1996.

Well, the problem is clearly that it is not.
(In case you are actually confused "duty calls" or "I hear the call of duty" (or "I hear the call of nature") can mean the speaker needs to take a shit.)

Kingdom Come 1 promised this as a mechanic but then didn't implement it. There are still toilets but you can only read books on them.

I remember in ARK you would periodically shit a sphere. I forget what it can be used for though. It is definitely a game mechanic :)

In this game there is a full optional nutritional/metabolic tracking mechanic, where you can leverage taking poops and use it to distract enemies, attract predators, or weaponize them to get other players in-game diseases

It is in the Sims. Including "The Sims Bustin' Out" which is an RPG.