In Sidonia no Kishi, why is it that the majority of the Gardes pilot are females? I'm fully aware that they have a third gender, however, most of the pilots are taking the female form. Why is that? Was it ever been explained? Does being female help them in photosynthesizing?
First, you can't make that assumption given that there are at least 256 pilots and we aren't introduced to them all.
You are most likely referring to the ones that we see around Nagate?
Using pilots we've "met":
Hoshijiro, Yamano, Samari, the 11 Honoka clones and Momose of the Akai squad are female.
(There are actually 22 clones, 2 batches of 11, but only the first batch are in the anime as far as I remember)
2 Members of Samari squad - Tsuruuchi, Tonami,
3 Members of Akai squad - Midorikawa's Brother, Akai and Aoki.
Shinatose is the neutral gender.
The sole cause of the unbalance is the clones, that's why most appear female.
[Why was a girl cloned? I don't know]
Note - For argument sake I've ignored all deaths.