If he is using the control panel to send his backup to a remote ftp site, I would suggest that you have him try and open up one of the backups. I have NEVER been able to get this function to work properly and send a full backup to a remote ftp site. It send *most* of the file and then crashes and you are left with an incomplete zip that fails when you try and open the file.
Consequently, the actual backup is left up on the server and continually takes up server space and eventually causes disk full issues.
However, to answer at least part of your question, yes, this backup is supposed to contain an MSSQL backup of any databases defined for the hosting account.