That's a shame. The difficult part for Nvidia is that as far as I know, windowed 3D support has to work via profiles and it's probably quite hard for them to keep up with the constant update cycle of an open project like Dolphin. The reason that the DX9 3D Vision hack works is that it forces Dolphin to run in "exclusive" full screen mode, which allows the Nvidia driver to more easily detect Dolphin. Honestly, I could probably make a similar hack for DX11 if the Nvidia driver works the same for DX11 applications...
The ideal solution would be for Nvidia to allow non-Nvidia developers to create these profiles but it doesn't seem like that's likely to happen.
I've asked on the forums but they only seemed interested in implementing it themselves, which is surprisingly nice of them, but it means that it'll break quite often.