Quickreply never signs up a user for email notification, and the checkbox on the full reply form is never checked by default. However, once a user has subscribed to a topic through a previous reply, there's no need to subscribe again. (Users can also edit their posts after initial posting to add the subscription flag.)
If you're still using the local SMTP relay, try and turn on any logging options it has. See if you can correlate entries in the logs with replies that users aren't getting notifications for.
You as the admin can also edit the first post in each topic to view the list of subscribed users - it'll be below the Options box on the edit form.
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