Where will this message be?
As part of update.php? Or in the UI somewhere?

From a user perspective, I think this is the wrong way around. They are Wikibase extensions. I would see it as a bug in the respective extension if it was released for a given version that had Federated Properties v2 enabled but did not correctly handle that feature.

As a practical matter it might be appropriate to notify developers of the extensions concerned sooner rather than later, if there's work they can do now to become compatible.