Received Notifications for Flow-replies (tested) are displaying <nowiki>'d templates in full, in email and special:notifications.
E.g. I wrote (here)
Test1 <nowiki>{{citation needed}}</nowiki> test2 <nowiki>{{welcome}}</nowiki> test3 ISBN 0123456789123
and received this email
and I see this in special:notification
(Note: Mention-notifications on wikitext pages are not affected.)