So, here is what worked for me :
I ran across the duplicate files issues when selecting a Synology NAS drive by choosing the network location drive in file history advanced settings.
I canceled everything and deleted all backed up data.
Then, I mounted the Synology shared folder as a mapped drive in Windows with Synology Assistant.
Finally, I restarted file history by selecting the Windows letter of the mapped drive as destination (not the networked drive - although pointing to the same device, of course).
All by magic, file history started to work normally (no more duplicates, and even the excluded directories seem to remain exluded).
Now let's hope that any temporary disconnection of the mapped drive will not mess my file history again... After a week, it's still stable.
If it may help anyone...that's great !
Michel