Surely male applicants wouldn't be scared off if most of the YC partners were female. Why assume female applicants are any different?
Ultimately, this is a pipeline issue--there are just not enough women founders who go on to be angels and VCs.
In contrast, there's 500 Startups, where Dave McClure is actively reaching out.* Which environment is likely to look more attractive to women entrepeneurs?
* http://www.ezebis.com/venture/dave-mcclure500-startups-found...
This is also why affirmative action hurts the careers of people who ostensibly benefit from it, if they don't get into Harvard: at Harvard, the black/white SAT gap is fairly small. Everywhere else, it's huge, so there's a big adverse selection problem, and of course employers know about it.
Because they have a hard time getting female founders, they have almost no female alumni to pull on. They want only the cream of the crop for this highly important role, and I can't think of a single female YC alum whom they think of as highly as they think of Sam et. al. Maybe Jessica Mah in a few years, but inDinero is too young for her to lose focus now, and she doesn't have as much experience as they're looking for yet. And I don't think they're comfortable inviting in people with whom they haven't worked.
This problem is a lot bigger than YC. It's not that women don't do YC, it's that women don't do startups. YC has a few hundred active startups to herd, and I think they just don't have time to address these problems of the larger startup landscape.
No insult to Sam, Garry, Emmet, and Justin who I'm sure are very talented. But given how Jessica Livingston talks about how hard it's been for Y Combinator to attract female founders and then they do something like this, I really have to wonder how much they're trying to change.