@Patriccck - there were some problems with beta cluster recently. I re-checked today (both cswiki and enwiki on beta cluster) - notifications can be marked as "Read".

I checked specifically "failed login" notification (as you mentioned it in the task description) - the "Read" status persists (as well as the "Seen" status). Also the issue was checked for both - in-wiki adn cross-wiki notifications. Closing the task as Resolved. If you'll see that the issue re-appears, you may re-open the task.