I would argue the other way around, it would be unclean to leave a reminder with a dead link in it. Who’s the originator doesn’t matter in this case, you can create reminders in any app be it the system Reminders app, a third party reminders replacement, or from within Agenda. We don’t make a difference as to which app creates the reminder, but your default Reminders app is the boss over reminders. Agenda merely links to them and removes the link when the note gets deleted again.
The same is true for Calendar events and the Calendar app, there it would be simply unexpected if the event would be deleted when you delete the note. Reminders are a bit more in a grey area as they are generally considered more light weight than calendar events, don’t really have other invitees and are also part of the note text rather than assigned at the note level itself. This grey bit makes it more logical to delete the reminder if it was originally created in Agenda, however we prefer to stay on the cautious side and not make this happen without any confirmation by the user so he/she’s fully aware why the reminder is suddenly gone from the Reminders app. As said, the solution would be to just ask at the time of emptying the trash what you’d like to happen.