As has been said before, PS4 is not using DX11 either. However, both PS4 and Wii U's GPUs are capable of DirectX11 equivalents found in OpenGL.
Aside from that, the whole argument is a red herring. Even if Wii U was only capable of DX10 equivalents, it wouldn't matter, none of the engines being created for these games require this API or that. They adapt game engines to the environment they are developing for. As they are adapting the PS4 version of the engine to be compatible with that platform, and vice versa. If this was a legitimate excuse, we would have never seen any multiplat on PS3.
This is a tactic being employed to discredit the Wii U as a platform, because everyone now knows that Wii U is more than capable of running all of the same engines that the other platforms will be running, thanks to companies like Crytech and EPIC, they are now trying to confuse people with talk of DX 11 like the PS4 is actually using it. Shameless.
As far as why they actually aren't bringing it to Wii U, I know that if I were Sony I would not want to have to compete sales wise with the Wii U with regard to KH3, and if I were Microsoft, I would pay anything to have it on XBOX if only to say "here's our commitment to Japan". Between the two of those companies, if it released on the Wii U the Wii U version would decimate them in sales. Nintendo fans are already partial to KH.
Another reason could be, seeing as Nintendo still seem to be figuring out how to use their new system, that the tools still aren't mature enough to enable the use of DX11 equivalents. This can also be seen through Unity, and they said in candid conversation that Wii U Unity will scale to DX11 equivalents, but it isn't there yet, Nintendo is already employing rendering techniques that were first seen in DX11 and it's equivalent OpenGL version (they are hard to follow).
So Nintendo has some catching up to do with regard to fully realizing the potential of their own system, and developing the tools to help developers, but there is literally no valid excuse for passing up the Wii U with KH3. Custom GPU or no, their decision was made purely due to their unwillingness to develop to custom logic, which is lazy, and will cost them sales in the long run.