Ok, so I couldn't figure out anything, but now while I'm writing this I tried ls -U, ie. unsorted ls, and found out that all the problematic dirs are in sequential order
I tested attaching another disk to QNAP, a disk that happens to have an earlier backup of the same CD FLAC rips... the same problems show there, ie. 10 unaccessible sequential (ls -U) directories under that subdirectory. Different directories this time, so it's not about the contents, but some other feature / index of those. Also on the same disc are a few other unaccessible directories, but that's the only directory with so many subdirectories that the "10 in a row" thing is visible.
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