Something that hasn't been mentioned yet is how 40k stacks up to other miniatures games in terms of female representation. After all, fluff solely exists to sell models and provide background to games. I don't have experience with any of them, but do any other scifi mini wargames display an equal mix of genders in their warriors? I'd say probably not. I've never seen female Pig Iron soldiers for example.
To me the reason for this seems simple: The modern military notwithstanding, human history has created a situation whereby the average person automatically imagines a male when they imagine a soldier, and automatically imagines a group of males when they imagine a unit of soldiers. This game (like all other wargames) is about soldiers. To make the models 50% female in order to reflect fluff would make a statement on an immediate visual level that the game designers may not want to make, i.e. it would challenge people's immediate, visual preconception that soldiers are male. The majority of people don't buy things that seem intuitively odd to them. Regardless of whether or not there is gender equality in the fluff or the real world, what matters is people's preconceived notions, and challenging them is generally not good business practice. You can't make fiction too realistic (especially not overblown gothic science fantasy) or people won't like it.
Which is all just a complicated way of saying that the reason there aren't many females in 40k when perhaps, reasonably, there should be is because a bunch of mixed gender soldiers looks weird to your average 13 year old boy and they wouldn't buy it.