We don't have an automatic pruner, but I think that is a great idea. Right now its ad-hoc, but I am going to add this next time to our administration site.
I've verified that topic subscription and forum subscriptions are working. There seems to be a 30 minute inactivity period though, meaning that you have to be inactive on the boards to be notified of the new topic or message.
Going forward we might prune subscriptions once every year, but I think we will go 1 year back, so actually the next prune will be in two years or when we reach an unacceptable # of subscriptions. 6,000 is way too many!
The reason we were getting some mail error codes was related to the # of topic/forum subscriptions we had!
Things are running good now!