They did a maintenance last night, which was likely the cutoff point.
Really weird that they let you purchase software that they won't let you download, though. I expect there isn't any recourse, given that you are free to update.
No, no! This is good! Remember how the 3DS wouldn't let you access the eShop if you weren't updated, wouldn't let you purchase a game if you didn't have the storage space to download it right there and then, and wouldn't even tell you how much space you needed if you hadn't added the funds to your account? It was a draconian process and it was a really big hassle when there was sales on.