I just realised that the password that is stored in the .mycnf and my.pass files are not hashed but are plain text passwords.
It is possible to access MySQL using ‘mysql -u -p’ and then use the password that is stored in these files.
Whilst I understand that it is posible to create PAM users and then create .mycnf files for them, I prefer to create actual mySQL users using either the MySQL console interface, PHPMyAdmin or Webmin (which I have installed for finer control over Apache and MySQL as well as creating new mount points for extra HDDs).
Also whilst I am considering installing extra hard disks, I have noticed that the backup module does not allow backups to be stored directly to a path which has a drive mounted on it. (eg /dev/sdb1 mounted to /media/backup)
Sure, it is possible to set a samba share to point to a mount path (but that seems a bit of an overkill if you are not using Samba for any other reasons - If needed, instead of using Samba to remotely access backup files, try using SFTP).