Thanks for the suggestion, after deleting the thumbnail cache with:

rm -rf ~/.cache/thumbnails

Nautilus is now correctly showing the embedded cover art for my existing
.m4a files.

To better understand the behaviour, I made an additional test:
1) I downloaded an .m4a file without embedded artwork
2) I added a cover image to the file
3) I refreshed the folder in Nautilus (F5), but the thumbnail didn't update
4) Only after renaming the file did Nautilus generate and display the correct 
thumbnail

This makes me think the issue might be related to Nautilus not
regenerating thumbnails for files whose content has changed unless the
filename also changes, so it could indeed be a caching behaviour rather
than a decoding issue.

In the past, I'm quite sure .m4a covers were not showing at all. My
whole music library is on a USB drive, and back then no .m4a file showed
a thumbnail, while .mp3 files worked normally. So it's possible that an
older issue has since been fixed, but the stale cached thumbnails
persisted on my system until now.

Thanks again for the help, I'll keep the rm -rf ~/.cache/thumbnails
workaround in mind for the future

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https://bugs.launchpad.net/bugs/2111560

Title:
  Nautilus does not show embedded album art thumbnails for .m4a files

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