Well, it's not really a matter of being "unconsciously sexist" or that they "against" strong female characters; it's more about business tactics and target demographics. Traditionally, companies target particular demographics according to market data and research and once a product proved successful, they employ various methods of advertising to promote sales. And the Beyblade anime franchise?...is, well...an episodic commercial series. So, it's not as simple as assuming that the TV show is "sexist" and more that companies see "this thing appeals more to this group than others; let's focus our resources on them." And it's maybe that this group doesn't include a strong female presence.
That's not to say that female player don't exist, it's just maybe there's just not "enough" of them for companies to devote resources to an weak demographic.