if that's the format you want or already use, then you can't use that drive for anything else, as it's a proprietary format.
If CEMU accept extracted format (code/content/meta) then you can use that format with Loadiine, which can launch extracted format located on HDD by using Mocha 0.2beta (it has FAT32 support and SD redirection to USB; but it's beta, could have issues).
Another solution is a little tricky, as it's still code/content/meta, but not using loadiine to launch the game but the console itself.
by using Mocha0.2b and tricking the console into thinking the FAT32 partition is actually a real WiiU formatted partition you could use the extracted content for both "wiiu" normal behavior AND cemu, but only if CEMU accept the games located in different folders.
I never used CEMU, does it expect games to be in a single "ISO" folder location? or could it load games located in multiple TitleID subfolders (path layout used by the wiiU)? As emulator, it probably reads internal system file layout without problem.