I have a domain with has mail only. The mails had amounted to 99mb. Quota is set on group and user and quota check is at 4am daily using crontab. Below is what VirtualMin is reporting.
Disk space used (including sub-servers) 732 kB (732 kB by Unix user, 0 bytes by mail / FTP users)
Space used by databases 8192 bytes (8192 bytes in this server, 0 bytes in sub-servers)
Machine running on CentOS 4.4, VirtualMin 3.23(confirmed version)