I think this is probably very genre specific. I suspect the nonfiction and realistic fiction boy/manly/macho genres(outdoors, machines, fighting, and the like) may have been especially cannibalized by games/video. I don't recall seeing any of this stuff on my last trip to a physical bookstore. But on the fantasy/geeky side there are more great options than there have ever been, and, as a girldad, I can tell you that female main characters are tough to find.