No plans to link Wii U and 3DS eShops
The Wii U and 3DS eShops are completely different entities. Although both stores contain content that relates to each other, they aren’t linked in any way.
Users can’t look up shared history between the two systems. It’s also impossible to, say, buy a 3DS game through the Wii U eShop. And that’s how it’ll be for the foreseeable future.
Nintendo of America’s Dan Adelman was recently asked about the possibility of linking the two eShops, but there are no plans for now.
“Well we’re calling them both eShop. It’s just that one is the 3DS eShop, and the other is the Wii U eShop. Wii U users can see info in the Wii U eShop about 3DS games, but right now we don’t have any immediate plans to sell 3DS games via the Wii U eShop – or vice versa.”
Thanks to Tim for the tip.