Standard albums or smart albums can contain the same photo only once, but It is intentional that Shared albums can contain duplicates. This is because we cannot edit the photos in the Shared albums - sharing a photo in shared album is like dropping a postcard into a mailbox. Once we post it, it is out of our control. If we want to update a shared photo we have to share the modified version again. All we can do is to delete the first version from the shared album, after making sure, that the other subscribers have save a copy, if they want to keep the older version.
I would not worry too much about shared albums right now and investing work into organizing them. Apple has announced major changes to the shared albums, to be released with the next version of macOS Golden Gate. I would wait until we know for sure what will happen to the shared albums in autumn, when Golden Gate will be released.
The duplicates in Shared albums do not count against our cloud storage, only the downloaded local copies will require storage on our devices.
To find duplicates within a smart album quickly, you may want to sort the shared albums by the capture date, so duplicates will appear side-by-side. The duplicates between Shared albums will be harder to spot. Are all shared albums shared with the same people, or do you have to check as well, if there are duplicates that with different subscribers?