I still don't think any of us are in a position to say that Nintendo don't know what they're doing, when they're outpacing the competition (except for Zynga and Apple) profit wise.
We CAN look to answer why they're doing as they are, which I think is more interesting, rather than assume that they're out of touch. They have an enormous marketing department, so whatever they do regarding rumors like weak hardware, they must have thought it the smartest move for some reason or other.
Personally, I don't really doubt that the Wii U in some regards may be weaker than PS3/360. The Wii didn't handle shaders quite as well as the first Xbox, and I'm sure if the development kits still run on NintendoWare, shaderprogramming will STILL be an issue to some degree.
The thing about the negative rumors is that it's such a small amount of people who circulate them, and such a small amount of people who care. If Nintendo open their big corporate mouth about the issue, EVERYBODY will have their attention drawn to it. Every fan, every investor, every news site, every potential future costomer.
Better not call attention to the discussion at all, as Nintendo at the moment seem confident that people will be pleased with Wii U's graphical prowess come E3.