I am an atheist, skeptic and a man of science (skeptical until hard evidence arises). But cynical is what I would be called in this period.
(Atheism is not a religion but I idgaf if you think I think about gods. I don't. Gods occupy 0% of my time. Also, I think you should stop this debate. No one will win because no one will acknowledge defeat.)
Atheists are there since the first religions were invented. Long before Judaism was henotheistic or the first Vedas. But it's anachronistic with CK2 because the term was not used. Deism should be in Eu4 but that's another forum.
I am a Christian, a skeptic and a man of Science - nice to meet you.
I think it's important to destinguish between Atheism as a belief an Atheism as a belief system.
To begin with - what is Atheism?
Atheism is not believing in a God - I say a God because Christians are technically Atheists - they don't believe in Zeus. That's important, because it demonstrates that Atheism is not actually a rational position, it can be arrived at by other means.
So what is Atheism as a belief system?
Atheism as a belief system is not believing in any God, or any supernatural forces, everything has a rational explanation. That in itself is not exactly a rational statement - for one thing you can usually throw out a weird coincidence or bizarre event that can't be explained by mundane mechanisms. The Atheist will respond to this nby saying "we don't know enough/don't have all the data". He cleaves to his belief there is a rational explanation even in the face of conflicting evidence.
That's not to say Atheism is unreasonable, it's as reasonable as Theism and like Theism there are intelligent and stupid positions.
How does this reflect on the CKII period?
Well, for starters there are no groups studying the Greek Atheist philosophy, both the Christians and Muslims are studying Aristotle and trying to synthesis his metaphysics into Christianity, Plato is largely neglected and the great atheists like Protagoras and Epicurus are so ignored that virtually none of their work has come down to us. It was not read so it was not copied, it may have been actively destroyed.
In India the situation is much more complex, and I am much less knowledgeable but I can say with some confidence that whilst early Buddhists did not believe there was an all-powerful God ruling the universe they generally DID believe that the beings worshipped as Gods existed.
So that's your general landscape, and frankly most people don't have a strong opinion one way or another on these matters - then or now. Atheism is as much a minority belief as it was a thousand years ago, as is really strong Theism. The difference between then and now is that we live in a very pluralistic society today - where people don't generally try to force things down your throat.
Go up to the average person today ask them if they believe in God and you'll more often than not get one of these answers:
"Well, maybe, I don't know."
"I'm not sure, but I think there might be something out there."
"Probably not"
"I like to think of myself as spiritual."
Question them further and you'll often find that even avowed Sceptics believe in things like "luck" or "chance" or some other odd superstition that's not entirely rational because we are not entirely rational beings. We tend to go with the general flow of society, too, and a lot of us will believe what "experts" tell us about a given subject without exerting a lot of critical thought, because we have better things to do.