Sorry but I think Kovid is exaggerating there.
Yes the Kobo relies on a database on the device to keep track of books / collections (shelves) / reading status etc. Yes; this database can become damaged but this is rare, and quite often can be linked to either older mods (for instance at one time 3rd party add-ons installed to the partition where the books / database are located, preventing an unmount of the partition when a USB connection was made), or to crashes of the Kobo.
I've used Kobos for years (since the original Bluetooth version) and have only had a couple of db corruptions (and I've probably seen more f/w builds than most people).
The Kobo utilities plugin has the ability to perform backups of the db, either daily or on every connection, and also can validate and compress the db.
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