I'm not particularly enchanted with the idea of an "Atheist" religion, more for mechanical and design reasons. Implemented as a religion, the following questions would have to be addressed:
- What are atheism's five major holy sites in the United States?
- What does it even mean for atheism to have high or low moral authority?
- What are the mechanical features of atheism? Can Atheist heads of faith grant claims? Can atheist priests grant divorces? Does atheism allow for polygamy, for concubines? Is atheism feminist?
- What are atheism's heresies?
- There are predetermined zealous-ness levels for religions. How zealous would atheists be? Should they actively spread the Good Word to the heathens, or do they not give a care?
These questions and more would have to be tackled, just to get a barebones atheist faith sorted out for the religions.txt file.
Further, CK2 is so geared towards religions playing a role in the game, there's religious terminology
everywhere. Even in the questions above, I mentioned atheists 'priests', zealotry, heresy, moral authority, holy sites, and there's many more facets than that to religion in CK2. You can't have a full-fledged atheist 'religion' without incorporating that stuff (it can work without heresies, I suppose), at which point you basically just have that one South Park episode where there's intelligent otters chanting "Praise science!" rather than an actual depiction of the rejection of religious belief.
It's much simpler to slap the cynical trait on a character and call it a day.