I'm not sure they're either over or under-represented is the correct way of putting it. For example, fighting games usually have a roster split of about 3 men to 1 women nowadays. Obviously, that's not parity. However, one can argue that the correct number of women in a typical fighting game trying to determine the world's strongest should be zero. There's no woman in the world that can hang with the upper echelon in MMA, boxing, or any other fighting sport of the kind. There are certainly women who can beat the living tar out of most men, but they're not on the same plateau of the world's elite.
However, there is a market to add women into these games anyway. And so Chun-Li and Sonya Blade get added to the rosters and are soon joined by many more. They're no where near the equal in numbers, but it's hard to say that they're underrepresented.
What's the correct number? Ultimately, that's probably up to the developer in trying to decide what's best for sales. Other genres are much the same.
That's the most realistic way of looking at it.
The gaming industry is a business, not a non-profit organization. The most important merit is the potential for profitability. Everything else comes secondary to that.
My mom used to read historical romance/mystery novels. She liked books where the main character was female and she preferred female authors. Judging from the landscape, I'd bet that she represents the majority. Does that make her sexist? Was she being unfair? As that industry is mostly comprised of a female audience, is it right that a female writer who writes about female characters has an advantage in getting a story published? Is that something we should look to change?
In business, the audience has the right to determine the success of the content. There is no "fair representation." It's natural selection.