I just watched both seasons of the Gunslinger Girl anime adaptation. I'm not sure if this is addressed in the show or the manga, but why are all the cyborgs female? I take it that they are kids because it's easier to condition them - are there any male cyborgs in the manga?
The simple answer here is that this is what makes up a "Fratello" team, an older male handler and his young girl cyborg. This relationship is a really important theme throughout the series. They are young because they are easier to condition, plucked from traumatic experiences so they can form a strong new bond with their handler who has complete control over the conditioning and how much is needed. Like with the instance with Triela, where she sometimes expressed a bit of a rebellious (for lack of a better word) tendency toward her Hilshire, understanding the situation she's in and what the conditioning does, her bond with her handler trumps everything. Also see: Elsa, where her bond with her handler was so strong that it went to extremes (death).
I remember reading somewhere that this sort of relationship was easier to control as opposed to an older Female (or male) with a young boy, where the boy could be less cooperative and obedient, but I can't find that reference right now.
To answer your other question: No, there were no male cyborgs.