Plugin deprecations, warnings and unmet dependencies are displayed in the "Manage Jenkins" and notification bar only.

From a user experience aspect, these kinds of warnings should be displayed in the update center too, especially if the update center offers you a bunch of plugins to update, but you want to address unmet dependencies or incorrect installations only at this time.
You'd need to either switch between the "Manage Jenkins" view or the notification bar, to see all warnings at a glance again.