Haven't read the manga, but at least in stand alone complex when talking about the accident and her recovery in third person, I feel like she was referred to as a girl, though I'm honestly not sure if that's important at all, the way she talks about herself in the adaptations I've seen, she seems to put her personality above everything else relating her past or identity, she is her actions, not her backstory (or that's how I perceive it in the versions I've seen, except maybe the first season of the latest one).