Like people are already doing right now? If every Wii U owner was also a 3DS owner there still would be more than 30 million 3DS owners without Wii Us, so little would change.
Unique libraries? The best selling Wii U games have 3DS counterparts that were released earlier.
Yes the point is that the Wii U having such a small install base means that the games released on it have a sales ceiling. Iwata directly says that the point of having a unified ecosystem is that they won't have to build install bases anew with every system.
It won't matter if the console SKU only sells 10 million and the handheld SKU sells 80 million because the games can still sell to everyone.