I am sure there used to be something like "You have no notifications." in an empty flyout. Now there is only an empty grey area.
Checked in betalabs - "There are no notifications." is displayed in all cases when there are no notifications.
Also, checked the case when a new user signs up to a foreign wiki and disables cross-wiki notifications - previously there were some hiccups like displaying empty placeholder for Alerts.
Now "There are no notifications." is always displayed for such cases.