Considering how awkward it is to use he/she pronouns in Japanese, I don't think there was any intent to keep it a secret. Again, Sypha's art is female. Sypha's portrait if she's Trevor's ally is female. Sypha's voice is female. The only way Sypha could be confused for a male was if she was a new-half. So if you really want to push the "Sypha is a he" or "Sypha looks like a he" issue, then you have to go along with the premise that Sypha was a gay transvestite. Every serious gamer knows US instruction manuals are not canon except when the characters in the games are of US origin themselves (e.g., Ninja Turtles, Mighty Max, Earthworm Jim, etc.).