Nintendo have confirmed that points purchased on one system, for example Nintendo 3DS, still can't be used on the Wii U.
In the Q&A session on Japanese website, a question raised was whether outstanding Wii Shopping points or 3DS eShop points could be transferred onto a Wii U. The short answer is no. The remaining balances must be used on the originating system. So if there's a pesky 100 points sitting in an account, it has to be either topped up or used.
With Nintendo planning Nintendo Network integration on the 3DS and mobile apps however, a more unified purchasing system and balance management could become available in the future.