I have recently opened a support ticket about the below issue but it seems that currently(Smartermail v13.3.5535) there is no fix for that and they suggested me to post the issue in the community for vote.
I hope others would find it helpful too and vote for implementing it in the next update/release .
Issue:
Domain Administrator account have the ability to increase the mailbox size limits for users to whatever size he/she wants and users can still upload files via FileStorage even if the domain disk quota has exceeded.
Note:
Users will not receive anymore emails when the domain's disk space has exceeded and they will receive notifications about that but they still can send out emails.
My Suggestions:
1. It would be nice to have a feature for setting hard limit for domains so Domain Administrators could NOT set mailboxes size more than the domain's disk-space limit .
2. Ability to control if the over-quota domains could send out emails or not.