NT backup for exchange is not supported (it's not the most robust backup system) - You're definitely better off with a proper exchange aware backup such as Veritas Backup Exec or the like.
That said, DiRT can be used for this type of migration with messages - the "200 mailbox" limit that has so profoundly confused everyone is put there as a warning that diRt is not an appropriate tool for REGULAR backups with messages (i.e. as opposed to a migration scenario where this is a one time move). So if you're just doing this as a migration, I'd go ahead and use DiRT (which uses ExMerge in the background).
If this is a situation where you want to be backing up messages on a regular bases, I'd highly reccomend investing in a good exchange aware backup package.
