When you have a file it occupies a certain space on the hard disk. When you make a file like a photo smaller and you save it then it uses less space like this:
That's not what happens when you use a database. Database files like Mail Archiver's archive are much larger. Writing such large amounts of data for every change would be much too slow. Instead the data is deleted internally. As a result after deleting emails from an archive the file size does NOT change. If you want the archive to get smaller after deleting lots of emails you need to do a clone:
Cloning reclaims the space that comes from deleting emails.