Well 1000 days is almost 3 years... geesh. When messages get that old, surely someone can either archive them locally or in a separate IMAP folder.
Hrm - I was thinking the files' ctimes would be updated when they were moved / moved back, however that doesn't seem to be the case from a quick test. If it's a shell user, you could "cheat" by using "touch" on ~/Maildir/cur/*
re: POP3 users... I would really not suggest that people leave messages in their inbox for very long using POP3. With POP, the messages should be downloaded to your email client(s), and removed either immediately, after some time period (maybe a week), or when deleting the message out of the local inbox.
If it's really important to keep read messages server-side, use IMAP instead. And in the case of POP3, it really /is/ a performance problem when a user has tons of old messages lying around.
This definitely isn't a perfect system (and I'm sure gentle suggestions for improvements / enhancement would be considered), but the bottom line is that if DH didn't enforce this, there would end up being a lot more performance problems with all users' mail. I do think it would be good to have a checkbox that says "please don't expire messages at all if the inbox has < 500 messages" - this lets people who keep a tidy inbox BUT like to keep some old messages around do so.