1) As jlees mentioned below, you need to look at the "subset of women hackers who also have some entrepreneurial drive" when looking at something like YC. The 4% doesn't really surprise me at all.
2) My observation is that women tend to be on a timeline about 5 years "faster" than men because of their biological clock. As in, they'll start thinking seriously of marriage and kids late 20's, early 30's whereas men will deal with this issue more like early to mid 30's. So their window for doing a startup is smaller.
3) This is a bit of a generalization, but the dynamics are really different when you have all-guy co-founders versus mixed versus all-female co-founders. With mixed sometimes personal relationships develop which can make things messy. And when you have a couple of alpha-females together, sometimes that can also lead to problems (for example, see the all-female startup in the TechStars Reality show). [These are just my own observations. Please don't flame me for this!]