A user may choose to receive both notifications and email for new posts to subscribed topics. In that case, when a new post is made, and the user does not have an unread notification for that topic, an email is sent.
The email contains a link that will, when clicked, take the user to the first unread post and mark the notification read. In fact, if the user simply visits the topic the notification is marked read; the user does not specifically ask for unread posts.
However, suppose a post is made, and the notification (or notification and email) is created, and then the post is deleted. In that case, visiting the topic will not mark the notification "read". The notification remains unread until the user clicks on the notification itself in the notification list. And while the notification remains unread no further emails will be sent for posts to that topic. This can cause users to lose track of subsequent new posts.
This is the one situation, as far as I can see, where visiting a topic will not clear a notification for that topic. If visiting a topic suffices to clear the notification when unread posts still exist, it should also suffice when unread posts no longer exist.