Yeah, really it just comes down to the publication the manga ran in that determines its demographic, and nothing more than that.
Now that said, while something can objectively be shounen, that's not to say that it can't borrow heavily from shoujo tropes and ideas, which Hanako-kun 100% does. There's so many big flowery romantic scenes here, essentially functions as a reverse harem (with one main girl and 3 or 4 other guys around here that all get their entertained as romantic partners), and definitely more of a focus on pretty boys being gay and pretty than in your...Narutos (and this isn't just "fujoshis being scary", there is no way that Mitsuba and Kou's arc is meant to be taken as a purely heterosexual "guys being dudes" thing).
Also should be noted that Hanako-kun was serialized in GFantasy, who also ran such shounen series as Black Butler, Pandora Hearts, Nabari no Ou, Aoharu x Machinegun, and The Royal Tutor, among others. I've always thought it was interesting that GFantasy is technically a shounen publication because so many of their series read like a shoujo than a shounen (and I do think the audiences do tend to be more female leaning).
But ultimately, does it really matter, I find the idea of categorizing shows by if their "boys/girls only", it's definitely a weird thing in anime. I guess if you think like "hell yeah brother I need some bad ass action shounens like my Attack on Titans" and only look at shounen then you may be shocked by the amount of variety allowed within the arbitrary confines of what's "for boys/girls/men/women" then it matters but otherwise...it's such a weird and pointless way to approach anime (and media in general)