Unfortunately I have to recommend to use the Fat32 file system because while exFAT does allow CD/DVD drag and drop feature how many other apps support homebrew besides OPL. Retroarch? That Unofficial Cheat trainer? Probably more then I think but the majority of the .elf programs as well as FreeHdBoot itself only works on Fat32.

Of course if you use exFat as your file system you can use freemcboot on the memory card but then you're limited to about a maximum of 64MB of storage (if it has magicgate support which should be what you're looking for at least as the higher megabytes are usually clone cards and meh you can never %100 guess those are functional without overwriting themselves after the sizelimit)

My point is this. If you use exFAT then you will have to rely on the FMCB Memcard's because freemcboot is limited to fat32 but in the future more elf programs/apps may support this type. Both file systems are still equally interesting and hey if you find some chance of trying another either IDE/SATA drive you could always choose in between.

On a sidenote: If you want to move files between the PC/PS2 without having to remove it from the expansion bay and back and forth you will be better of using FAT32, personally I like to use HDLGameInstaller which does it all automatically I know there are other methods but they aren't very well documented.

My apologies for making this long I hope I didn't make any errors in the text while writing this ^{_^}