I have an HDD where I store my digital WiiU games. Can I use it for storing cube games as well?
I don't think so. Your HDD needs to be formatted to FAT32 to be able to use it with Nintendont (and most Wii loaders). AFAIK, the Wii U formats the HDD to something else (either NTFS or a propietary format, I don't remember).