I think there are more atheist guys than there are atheist women, but I think it's a bit easier for men to set themselves apart from other people and to be independent than it is for women. Women may not be as gung-ho about describing themselves in a way that would likely be perceived as being divisive and unfeminine.
I would prefer to call myself a humanist rather than an atheist; being a humanist is more descriptive of my overall approach. Many online dating services don't give people the option of calling themselves a humanist, however, and if that's the case, then I'll call myself an atheist (based on not having a belief in a supernatural force).
I've gotten so many ridiculous contacts from online dating services (from guys who clearly didn't even bother to read my online profile at the service) that I've gotten more explicit about my atheism and I say that highly religious folks shouldn't contact me. If the guy talks about how important his faith is in his email or profile, I know right away that he hasn't even read my profile. (It still amazes me how many men on sites like Mate1.com think it's going to work for them to cast a really wide net without even reading any woman's profile.)
One doesn't know if publicly saying one is an atheist does scare off some perfectly decent human beings, of course. However, I think online dating might as well start with people who can accept you for who you say you are.
Theist guys are creepy, that can keep both the theist and atheist women away.
I put a personal ad in CL, I took a long time trying to figure out the most friendly & light-hearted way of saying I'd prefer an atheist, (as if I should have to do that) and I still got some really vicious and grotesque hate mail. Christians are geniuses too, revolting hate speech IS super-convincing, I almost changed my mind about atheism when I saw what I was missing there. Good stuff. My addy was anonomized, theirs was not, of course, and some of them seemed to expect me to write them back.
Now I'm trying to weigh those "spiritual but not religious" descriptions, that can mean just about anything. I tried Freethinker Match, but there's not a big enough pool of people on there, I'm not interested in a long-distance relationship, unless it comes out of a normal in-person relationship with changing circumstances.
I think many atheist woman are more likely to put 'other' or leave blank the religion box not to be too deterrent. For example, the atheist lady I just met put 'other, and quite serious about it' for religion on OKC, so I was very cautious at first when I saw that. Turns out other = atheist (whew).