that's not how you "install" a homebrew.
nintendont is not installed into USB Loader GX.
You only need to copy the nintendont boot.dol to your SD card. this is how you "install" homebrew. there's no installation, it's only a file on SD loaded when needed.
go to nintendont thread on wiiu > hacking (or usbloaders) section, read the installation section.
you need to copy files here :
sd:/apps/nintendont/
inside you need at least 2 files : boot.dol and meta.xml
That's all.
USBLoaderGX is already looking into this path by default for gamecube games.
just be sure you enable display of gamecube games (main window > top menu > 4th icon > gamecube)