I'm seeing the opposite. They've been using "Forbidden Scrollery" as the title since the beginning; cuc mentioned it on the first page. Yen Press titles are generally either entirely translated titles when they can or use some of the original title if that's how the work is generally referred to already. FS doesn't have this problem since basically nobody in the english fandom calls it Suzunaan, and there's no way "Touhou Suzunaan" would be translated, so I can easily see the logic here. I don't think missing "Touhou" from the title will mess up searching at all because of how unique the title is, even though personally I prefer the full title.
I think it's basically guaranteed at this point that the book being part of the Touhou series will be made obvious. The Amazon listing for vol.1 didn't give much info, but if you haven't noticed,
volume 2 is now up for preorder as well, with the description
"In the mystic realm of Gensokyo, library worker Kosuzuna awakens to her ability to read demon books. This volume crosses over with the games Double Dealing Character and Hopeless Masquerade of the Japanese hit franchise, Touhou!"Additionally the book series is now listed in Amazon, where it is called "Touhou Suzunaan - Forbidden Scrollery. Book Series", even including the fancy period which basically nobody pays attention to.
"Kosuzuna" aside, they explicitly say it's part of the Touhou franchise. They use "Gensokyo", and most importantly it mentions it overlaps with events of DDC and HM; this shows they're aware there is extra context required to understand the book, which bodes well for priming readers to acknowledge that the book is part of a larger body of works. Manga in general are not averse to having forewords and afterwords by the editors, and if they follow this (admittedly small) trend I figure the back cover and some sort of word from the editor would establish important things about the overall series. Some more rudimentary details about the setting and characters are also given by the margin notes in the original manga (filling in basic details about the setting is their whole purpose), which I assume will be included.
You could say I'm reading too much into this from little information, but I think there's more evidence for being hopeful they'll handle it fine than evidence for being wary.
EDIT: Actually looking at my tankobon there are no margin notes so they probably won't be included here either. Oh well.