Thank you very much for this extensive reply. I access CIFS shares using a low-level mount (with fstab). Setting metadata plugins in this order: Id3libMetadata > TaglibMetadata > OggFlacMetadata fortunately fixes the problem for FLAC files (it now uses TaglibMetadata). However, in the case of MP3 files (I suppose the program is using Id3libMetadata), files stil get re-written, although the program does not hang anymore, so that's an improvement.
Modifying cover art is very slow