Yamato is a female. The problem with her isn't that she identifies as a male, it's that she identifies as a specific person, in this case Oden who was a male. Yamato herself doesn't seem to want to be trans, given by the fact that she seems to make no effort to hide or get rid of her female attributes. I have a feeling that Luffy will get annoyed by the Oden Schtick, and just say he's going to call her Yamato. At that point we can see whether or not she wants to refer to herself as male or female.