Is this a virtual server? If yes, then it might be that the harddisk usage can not be displayed, as the Linux "repquota -avug" command does not display it under OpenVZ.
I have had sites de-activate when over their quota so ISPConfig3 knows that a site is over quota it just doesn't display them.
Here you mix up traffic quota with harddisk quota. Deactivate a website is for traffic quota and not harddisk quota.