Now if we're speaking specifically shonen then yeah the issue exists.
I'm talking about shonen series. Of the shonen I can think of, FMA I guess, Soul Eater and Medaka Box (duh) have the most representation, and by representation I mean that they are there and actually do shit. Nami and Robin don't fuckin' do anything but have bad proportions. When you look at the Big 3...
One Piece -
Strawhats - 9 members, 2 girls, 7 guys. Robin and Nami do nothing. Well, OP has evolved so that Luffy is Goku and Zoro is Vegeta so I guess they are in line with everybody else!
Shichibukai - 7 members, 1 girl, 6 guys. This gets even worse then you consider that there have been 11 Shichibukai we know of and Hancock is still the only girl.
Yonkou - 4 members, 1 girl 3 guys. That's ok I guess, but Big Mom is probably some ugly monstrosity.
Naruto -
Akatsuki - 11 members, 1 girl, 10 guys. Lol.
Kages - 5 members, 1 girl, 4 guys. The Kages switch around a lot but I think the Mizukage was in all the meetings and I don't remember other girls.
Bleach -
Captains - 13 members, 2 girls, 11 guys. Lel.
Espada - 10 members, 1 girl, 9 guys.
Vandenreich - I cannot be assed to remember how many members there are in this shitshow.
I don't know what I'm trying to say other then most of the time it seems like a girl is thrown in as a token thing. Even then, the S Ranks in One Punch Man are 17 members, 1 girl, 16 guys. At least Tatsumaki is the most important one I guess????