Thats rather the point though - PCs are getting hired to hunt down those minor cults before the grow to be big cults. Thats the premise of the Conan the Barbarian movie and Conan the Destroyer and Indiana Jones and the Temple of Doom and ...
I did a campaign once in which the PCs were all part of the Inquisitors in Mother Church and were charged with recovering Holy Artifacts and hunting down evil cults and heresies
That is a cool idea, especially if you build a world with a monotheistic god or dual deities.
I think the OPs trying to say that the thing to use cultists for about every second issue is a bit overused.
To go back to those FR and GHK deities of evil: Ok let us take a e.g. temple of Nerull, given that it is a known location, maybe the ruler does tolerate it, is the priesthood and those who attend it a cult?
Maybe those are simple people who want to appease the god of death so he let's them live.
It becomes a cult when said temple starts to sacrifice the population and mass produce undead out of their corpses but before that it is just a temple of an evil deity.
Let us compare the cult of the dragon, I am not very well with its lore atm. I think they praise Dracolichs, I might be wrong here, but it is something about that as far as I can recall. But that is not the point, the thing is, a dragon, or a dracolich or whatever mob does not need a cult to be a dangerous and cunning opponent. If you want to add minions as his servants, a tribe of kobolds or Ogres perfectly does the job.
Same with a crime syndicate, it is not necessary that the leader is in truth a priest of a hideous demonprince who plans to take over and rule the world with the help of his thieves guild.
It is far more plausible that the leader of a thieves guild is a rogue himself who got into this position than someone else. Ok, ok, Xanathar is also a cool idea, but his thieves guild is just that, and not a beholder cult.