I use FAT32 now, but I used to use exFAT. The experience was unpleasant.
Since this isn't even a switch-specific problem but the FS itself having zero resilliency (as any developer familiar with filesystems could tell you), I'll share a few anecdotes.
Once upon a time, I had a huge number of CBZ (comic book zips) stored on my phone's 256GB SD (formatted exFAT.) One day, suddenly, more than forty of them were randomly corrupted. According to exfat-fuse, some clusters went missing. Therefore, I tested the disk. There were no hardware issues.
That's what regularly happens on my phone with exFAT. I keep it formatted that way, since using ext2 causes permission nonsense due to android giving every application a different UID.
Now, with my switch? The sdmc:/switch and sdmc:/Nintendo directories regularly became completely corrupt, and beyond repair. So I copied everything valid to my PC, reformatted, and copied back. After about six times of this, I simply gave up on the filesystem. FAT32 has a backup FAT for in case stuff goes wrong, and thus far FAT32 has always been repairable on my switch.