USBLoaderGX doesn't make any difference if the drives are stealth or not. Everything work the same way.
If you have an issue with 2 Ustealth HDD, you'd have the same issue with these two exact same drives even if they weren't Ustealh'd.
Your problem is probably a setting problem.
edit:
your thread title is probably confusing. I thought you had "2 Ustealth HDD".
But I understand that in fact you have 1 stealth HDD (for vWii mode) and 1 WiiU HDD (for Wiiu mode).
The order and USB Port you plugged the drive is important.
vWii HDD data cable requires to be plugged on USB Port 0 (back-top port).
the WiiU HDD can be plugged in any other ports, as long as you have an updated nintendont (which skipp the WiiU drive, or else it will not find any games).
Then, you need to use cIOS r52 (NOT r53).
You also have to setup all paths correctly, and enabled the display of Wii and GC games (4th icon in top menu).
Do you have Wii games on NTFS and gamecube on FAT32 ? or all on FAT32 ? or mixed Wii on both NTFS and FAT32?
the Wii partition should be selected under "settings > hdd menu > game partition"
the gamecube partition should be selected under "settings > user's paths > Gamecube Main folder" (USB2:/games/ if your FAT32 is the second partition)
If only some games are displayed, then it's probably another setting related to filtering the games by categories, or by parental control level?
you could try to reset all the loader's settings (or make a backup in case you don't want to lose them) just to try if the issue are the settings.
It's also possible the problem is your file's location and filename.
Nintendont might be compatible with more paths than the loader.
Be sure to use the correct path layout :
/games/Title [ID]/game.iso or disc2.iso
do not use :
/games/game.iso
For even better compatibility, I recommend you use SD card for all your homebrew's data, don't use your USB's FAT32 partition to list homebrew. (boot.dol, and all resources should be on SD)
Thanks for the detailed response, the WiiU is at my friends place but i will try everything you posted.
I have the USB plugged in the correct spot, I removed the WiiU HDD and tried to get the games to display in the loader, no deal.
Which is strange because the gamecube games appear in nintendont.
I have targetted the correct directory as you stated.
I spent along time looking thru the filters/settings. Its strange that some games appear/don't appear!
I followed the sticky for my cIOS installs so i have to check which ones i installed.
The NTFS partition is for non-wii files, has some movies/etc.
I have the correct setting > hdd menu > game partition on.
I have tried setting multi-partition to on and off, makes no difference.
I set it to look at the fat32 partition and not the NTFS.
I have the path layout for GCN games correct, it was working fine 2 days ago. Nothing has changed other than the wii being turned off and on.
Last scenario i can think of is the HDD corrupted somehow since the y-cables are plugged into a wall socket and even once the wii is off, we have to manually turn off the wall usb power??
I will have to check the hard drives when i have the chance.
Anyway, appreciate the advice, will get back to you once i do another proper pronosis with the WiiU at my place!