According to the Club Nintendo website, “Due to certain system constraints, Club Nintendo accounts cannot be linked to the Wii Shop on the Wii U. Games downloaded through the Wii Shop on the Wii U (in Wii mode) do not qualify for surveys or Coins.”
What this means is that downloading a title from Wii Shop on an actual Wii will net you Club Nintendo coins and allow you to do more surveys which can lead to more coins. However, downloading the same game, linked to the same Club Nintendo account onto a Wii U will get you nothing. Meanwhile, buying games on Wii U’s eShop also earns coins. So, it is just Wii Shop games on Wii U that have this problem.
We don’t know what exactly this “system constraint” is, but hopefully Nintendo will find a fix to it sooner or later, because right now everyone who decided to move all their Wii gaming to Wii U are getting the short end of the stick.
Source: Nintendo Life