Kobo have fixed the problem in the past. It happened late last year or early this year. Kobo fixed the code running on the servers but needed some information from the users before they could fix the actual shelves. In my case, they had to remove all the shelves from the server to fix them.
This occurrence is seems to be different. The last time, there was nothing I could do to fix it on my device. A sync would just bring it back. Now, as you mentioned, you can play with the database and clean it up. And then a sync will clean things up. That seems to be working here. Though it has happened a second time but after a month or so. Also, the shelves aren't actually duplicating. They are rising from the dead. From the timestamps involved, it is actually shelves that have been deleted and are now coming back.
In any case, Kobo do know about the problem. It has been directly reported to them. It has been indirectly through other places and Kobo people do read this forum. But, they don't participate nowadays.
Also, I took the "opportunity" of having the duplicated shelves to add a function to my Kobo Utilities plugin for calibre. This will update the database to clear the duplicate shelve. I should be releasing the it later today.
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