Wow, that's really quite amazing. How are you viewing all of your purchases? I'm looking at my purchase list on both systems and only things after the NNID update on the 3DS are viewable.
Sorry, not the purchase list you're thinking of. Saying "purchases" was probably misleading, since I was thinking of play history. The Miiverse app, for example, definitely recognizes games you've played on either system. So I apologize for running away with talking about "purchases."
What I should have said was "account information is not tied to hardware, as we can see from things like play history in Miiverse being viewable on either device. This applies to purchases, too, with the caveat that there's no way for consumers to authenticate/redownload our accounts/purchases on additional devices (only one of each type of device)."
I'd have to check again, but a good way to know whether the eShops recognize purchases on both systems would be to see whether it clears 3DS games from your wish list on the Wii U shop when you've purchased them digitally. I *think* the Wii U shop automatically bumps games from your wish list when you buy them digitally.