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If you update your Kobo firmware before Calibre gets an update for that firmware, you'll always see an "unsupported firmware" error. If Kobo didn't make any changes to the database, it's safe to use Calibre normally. If Kobo did make changes to the database format, you may corrupt the database.
It's a "use at your own risk" type of situation. If you want to avoid such Calibre errors, then don't update your Kobo until Calibre also has an associated update. Kobo doesn't change the database very often, so it's usually safe to ignore the error, as long as you keep database backups just in case.
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