Yeah boxes could get flooded.
Usually that's what PMs supposed to be for. In a thread you should try to reply to a thread and address everyone rather than a reply to the topic.
As soon as I log onto the site the first thing I do is check my thread subscriptions in my userCP so I can check up on the replies to threads after I replied to them. It case you don't know the default setting are as soon as you reply to a thread you subscribe to it.
If that person that replied really didn't want to read that thread or follow it, then you can unsubscribe.