I was playing around while investigating the IDE problems in minimig and did some performance tests.
dd if=/dev/zero of=/media/fat/testfile.tmp bs=1k count=$((40*1024))
writes an empty 40MB file... on the exfat partition the speed is less than 400K per second. On an ext4 partition on the same SD card, I get over 10 MB/s even on long (800M) files with random content (/dev/urandom).
On the minimig side I do not see any speed difference for hardfiles (hdf) on both partition types and also the reproducible problems stay the same. So right now it is not a real problem, but with increasing performance of the cores it might become one.
To get a better performance when manipulating files on the Linux side, I did split the exfat partition and make an ext4 partition for all disk images. Those can easily be linked to /media/fat/, where MiSTer will find them.
Since removing the SD card from the de10-nano is quite a fiddly task, I would guess, that not a lot of people will plug the SD card into a Windows PC for file transfer.