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.
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There's also a JS error when the API request fails (HTTP 500 in my case because I was messing around with ApiEchoNotifications.php). I fixed that, but the flyout is still empty.
Change 291672 had a related patch set uploaded (by Catrope):
Fix JS error when API request errors
Change 291834 had a related patch set uploaded (by Mooeypoo):
Display error message on API failure or empty result
Change 291834 merged by jenkins-bot:
Display error message on API failure or empty result
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.