In the old games (.hack//INFECTION, .hack//MUTATION, .hack//OUTBREAK & .hack//QUARANTINE) the player Kaoru Ichinose created the character Elk. In one of the novels based on .hack//G.U. an opponent confuses their party with gender stereotypes--but Kaoru/Endrance is immune to such talk.
I also want to add: In the TV series .hack//SIGN Ann Shouji/Tsukasa is gender fluid. In the manga .hack//LEGEND OF THE TWILIGHT BRACELET Hotaru (real name unknown) was born into a male body but finds she can be a girl online.