Guest Poster, nothing about my answer ? are you okay with my nuance or not ? (I ask because you seems to very well understand Hanako since your amazing fanfic Sisterhood)
I'm hardly an authority on her. My interpretation of her is merely one of many.
Anyway, when Hisao confesses to Hanako that he loves her, she replies that she's wanted to hear that for so long. Since her route only takes 6 weeks, it suggests she picked up feelings for him quite quickly.
If I had to think of a reason Hanako would quickly pick up a crush on Hisao, I'd say it's a sense of familiarity. Of all the girls Hisao can date in the VN, Hanako's the person most similar to himself or rather, most similar to the way Hisao is at the start of Act 1.
At the start of the VN, Hisao is a messed-up kid who used to live a normal life until one bad day changed his life forever and during his long hospitalisation, he was essentially abandoned by the people he thought were his friends, leaving him rather cynical and depressed. When he arrives at Yamaku, he merely focusses on getting through the day, has no plans for his future and is rather passive, relying on his more assertive classmates to drag him into activities. Where games are concerned, he's playfull competitive, though not as overly as Shizune. (unless he starts dating her) Aside from games, he also likes reading. He's not overly social, even before his incident, he didn't have or felt like he needed that many friends, but he valued the ones he had. He hates the idea of being disabled or pitied, is very uncomfortable about the subject of his condition and dislikes the idea of other people learning about it.
I'm describing Hisao here, but this is basically also Hanako in a nutshell, it's just that Hanako is more extreme. Hanako's insecurities tend to cloud her judgement, but when they don't she can be pretty perceptive. It's quite possible that when they first started talking to each other, Hanako picked up a vibe from Hisao that she couldn't quite explain at first, but nevertheless felt familiar to her. She basically came to see him as a kindred spirit who was, in many ways, much like herself and because of that, it's not all that hard to believe she quickly took a strong liking to him despite her shyness.