ZUN is actually a pretty decent writer. I mean, he's good enough to get so many people to buy into his tidbits of lore that he tosses out here and there and turn them into a massive sprawling enterprise of fan canon and doujin :V
At any rate, they've stated ULiL is a full sequel, while Hisoutensoku was advertised as an expansion pack, so odds are good that the HM cast will have full story roles, and that you will not have to own both (Much like how you don't need to own MiAP to play as its cast in SWR). As for why Hanako's mentioned in the coding - likely because her sprite's in the game, and they referred to her by her name in the coding because they figured nobody'd dig through it (those assumptions people). Having only one new touhou isn't exactly unheard of, either - SWR's the only one that's had two newhus. MaIP also lacked any real "semi-final boss," so it's not impossible we might just have different stories this time around. Right that was Yukari, my bad.
That being said, this isn't actually the first time Hanako-san has been referred to by the games. Double Spoiler 12-6 "Hanako-san in the toilet." A nue spell card, so makes you wonder if she'll be shipped with Nue. And as for the concerns about the strangeness of using Marisa's Strange Last Word, it's likely that, assuming this is true, ZUN is treating the Hanako-san that is the hand in the toilet and the Hanako-san that is the girl in the bathroom stall as separate people (Which would still be rather strange but its own brand of strangeness).