WiiU Pro controller:
Nintendont can play games with the WiiU Pro controller.
USBLoaderGX has WiiU Pro controller support "inside" the USBLoader interface : It does NOT allow you to play Wii games with that controller.
WiiU gamepad:
Nintendont can be played on the WiiU gamepad if you inject the program (or the forwarder) into a WiiU WiiVC channel.
USBLoaderGX interface can be used with WiiU gamepad too, but it's only beta as of today (1269 mod03). It will be released officially with 1269 finale version. Again, it's only a support "while inside the loader's interface", not to play games.
You can use USBLoaderGX as GUI to launch gamecube games with WiiU gamepad support (inject USBLoaderGX forwarder into a WiiU WiiVC channel instead of nintendont forwarder).
Note : When using the wiiVC injected method, USB is disabled ! you can only launch games located on SD card.
Gamecube adapter :
You can connect it to any USB port.
The homebrew HDD need to be connected to USB Port 0 (bottom port on Wii, Top-back on WiiU). Remember, USB is working only if you launch vWii mode, not WiiU WiiVC.