I don't have same experience, but I would upgrade without doubt.
Just like PHP 5.2 was forced upgraded to 5.3 or 5.4 at many hosting server, I personally believe MySQL upgrade will be the same in the future.
You've already received the message to upgrade MySQL database, it is a good time to do so. I believe next version of the same plugin/theme update will elevate warning message level.
Unless all your 30 sites are on the same server, starting from just one site and get some first-hand experience is always helpful.
