Many have had issues with modified / compressed / shrunk GameCube Images.
I would not TOUCH a WBFS Formatted HDD. Bets to use FAT32 or NTFS
A GameCube ISO fits fine on EITHER a FAT32 or NTFS HDD so feel free to use either. (They are small enough to NOT worry about shrinking or the like). Many use FAT32 and convert their Wii ISO files to WBFS format. If the WBFS file is still above 4Gb and they use FAT32 then they split the file in two and can still play perfectly fine from a FAT32 HDD.
This thread has info on splitting files: viewtopic.php?f=4&t=1346
- not sure which page. Again - you only need to split files if they are above 4Gb in size and you use a FAT32 HDD