i know what its like to wait forever for something like this, so i just checked right now.
have my wii u setup to launch all wii and wiiu and gc games from the external hdd (two usb ports at the back). gc games boot through nintendont. mayflash adapter using the two front usb ports.
I launched smash bros melee with gamepad support and no tv. gamepad took player 1 spot, gc controllers 2, 3 and 4 all worked. i selected a character with each one.
Tried it again with a tv, instead of gamepad support, and all 4 gamecube controllers worked, but it required me to have my wii u connected to a tv and have atleast 1 wiimote nearby. couldnt do it without a wiimote.
Please let me know if this was a sufficient enough test.
Unfortunately, i cant test your usb extension scenario though as i dont have a usb extension. i want to say it will work, but i do know there is a threshhold. i remember when using a usb extension with my older DJ equipment (maybe about 8 years ago), sometimes it doesn't work efficiently but this is a less strenuous scenario, plus the times have changed quite a bit since then.