Just a quick update to the situation. I didn’t mention this, but the folder in question was my Joplin notes filesystem sync directory. It contained ~11,000 files split into two folders - one with 7,000 files and one with 4,000 files. As already explained before, it sometimes took as much as 30+ minutes to scan through it.
I’ve since then archived quite a large number of old notes that I no longer need to view on a regular basis (and especially not on the phone), and also reduced the period of keeping note backups from “90” to just “7” days. All this has effectively dramatically decreased the overall number of notes to just ~2,100.
As a result, it now takes Syncthing just ~5s to scan the folder on a fresh run. I still find this quite strange, as proportionally it should take 5-6 times less to scan the folder, and not 360 times less 
. I’m not complaining, of course, but something seems incredible inefficient in how Android 11 handles folders with a large number of files in them. It’s not the file size either, as in this case, the size has actually increased due to adding a few large attachments to the notes.
All in all, the problem has been worked around on my side for now, but I’d like to let this topic serve as a warning for others who experience similar performance issues in Android 11. I also keep mentioning Android 11 only here, as the I/O performance issues are supposed to have been fixed in Android 12, but I can’t really verify this claim myself.