It's probably because „Is it any faster, I bet you'll ask? Well I can't tell..."
If you're interested in filesystem experiments I've posted a hack in another thread that allows you to use ext234 for mmcblk0p3.
https://www.mobileread.com/forums/sho...10#post3003110
There should be nothing wrong with FAT32 though. Well, other than if you actually fill that much with books, the Kobo database will grow gigantic and that'll probably cause slowdowns that are not filesystem related in any way...