It's not just C.SE that has this problem. It's not even just the SE network that has this problem. It's the whole Internet.
The anonymous nature of the Internet has made it easy for people to harass women--they see an obvious feminine username on a chat room/forum/etc and make comments directed at the user, knowing full well that there (usually) isn't any way for the user to retaliate. No need to go into details here, we all know what I'm talking about.
Obviously, someone who has been/expects to be treated like this will (a) not touch the Internet, or (b) Not make her gender clear.
Couple this with the fact that most SE site users are primarily programmers (and IT is a male-dominated field), and you sort of get an idea why we don't see many women on the network.
The suggestion of having them identify themselves will be detrimental--it sounds discriminating and will just make the ladies more wary of the Net.
I don't know how to fix this--looking at the reasons behind this, I can't cook up anything.
Wikipedia has had a similar problem, and they did put effort into correcting this. They were only partially successful, I remember seeing some reports on it (and hearing about it internally), but nothing big. Unfortunate, really--but you can research their efforts and try something along those lines; learn from their mistakes.
If you do manage to cook up something tangible, be sure to let the rest of us on SE know--I think this is applicable network-wide.