I noticed the exact same thing this morning, and had a mini-freak out. But then I noticed something:
The number of add-ons that I purchased showed two, but when I clicked on the add-ons it showed only one: HW. Like everyone else, it showed I hadn't pre-ordered SB, even though I had, but the fact that it was saying I had a second add-on that wasn't showing was weird.
So I tapped down past the avatars to the new bonus theme from the CE pre-order and clicked on that, and it took me to a new page that showed the Stormblood pre-order itself, and had a countdown timer for the download. I think it read 1 day 11 hours and change, off the top of my head, and it was counting down. So while the pre-order wasn't showing on my game page, and the store seemed to think I hadn't ordered it, it was still showing as a countdown to download.