The gender of Disciple/Handmaiden matters insomuch as it ties into how they react to Atton/Visas later on. I don't think it's too much of a spoiler to suggest that they were going for love triangles there and that, back then anyway, I don't think gay characters in Star Wars was a possibility.
I remember there was a mod to make Handmaiden recruitable for female PCs, but I figure that must break the Restoration mod.