As well known, the edb and stm files are not getting any smaller when deleting mail or mailboxes from the server; it requires offline defragmentation to get rid of unused space in the mail archive.

I am using ntbackup to backup the mail store, and I am just wondering if the data backed up is only the used space in the archive or if it also includes the unused space and make the filesize on the backup media the same as the size of the edb and stm files on the hard drive.

The mail store size is dynamic, so your backups will only require the amount of space currently be used by the Exchange database files.