Maybe they didn't add it to Gathering Storm due to it being hard to balance? I know that volcanic eruptions can be pretty devastating to a city and remove a lot of population but that usually tends to happen on very specific cities (aka ones that are built very close to volcanoes). A disease mechanic like the one in the Black Plague scenario would have a similar effect to that but to entire empires. It would stall city production and expansion for a while, specially since cities usually need x amount of population to build new districts. Not only that, it could mess up the whole golden age/normal age mechanic they have going on (although I am not 100% sure how they measure the turn length for each era now).
Personally, I would love a disease mechanic in the game, especially since it was something that was VERY decisive in history, but I can see why they didn't add it since it would be a bit tricky to balance it. Although it could be a bridge to some new items and buildings in the game. For instance, it could be a reason to add some sort of Medical district (which personally I would have a public bath, hospital and medical lab buildings in it), and maybe even a more advanced health mechanic like the one seen in Civ: Beyond Earth (although that was pretty much just a modified happiness mechanic from Civ 5).
Anyways, that is just my 2 cents on a potential disease mechanic lol
