I had this exact issue on both fat32 & ex-fat EVENLY on a several SD cards, and after lots of testing trying figure out causes card to become corrupt, i came to "my own" conclusion the same corruption issues would re-appear evenly on both fat32 and ex-fat on my cards and that the filesystem is not the problem, the problem was three things, the first problem was certain home brew apps are capable corrupting card, such as early of builds NX-shell, RetroNX (in my case), the second problem is the SD card, because my SD cards were of slower read & write speeds ,it takes longer to access a file causing the card to heat up and the card could not keep up with the switch and would cause a write and read error (corruption). Even under moderate usage,switch running games and home-brew at some point the card becomes corrupted. The corruption made files and folders on my SD card not browse-able, completely disappear, change in file size, and the files become unload-able because they have become corrupt. The third issue was heat, if card gets to hot due your environment being to warm, this will definitely cause corruption. if the card is reading or writing too many files consecutively, this can cause the card to heat up and cause file corruption. And lastly the Dock, the dock is capable heating up your card big-time due to lack of ventilation.
My solution, i upgraded/bought a high end ultra high speed II card, made sure my card doesn't get hot and for 5 months now, i been corruption free, and never having use fat32 again. Out my testings and experience,the problem was the Card, certain home-brews, and heat were the culprit and NOT EX-FAT.
Hope you and someone else can find my experience useful.
