There’s no need to enter a key for Visual Composer/WPBakery, it asks for those users that buy it as a solo-plugin.
We license it for all our theme users as we already bought extended license for it. No need to worry about license.

It should work perfectly, though the notification is annoying admittedly.
Whenever there is a new update for theme we always include the latest version of Visual Composer/WPBakery too, so in the next theme update will be included 🙂