Running "du" gets you a smaller amount for email than the cPanel interface is reporting. This difference can be significant.
This is caused by the setting "Compress Messages" being selected in WHM Home » Service Configuration » Mailserver Configuration. When this is set, the size of the messages on disk is a smaller, compressed size, while the amount reported by cPanel remains the full, uncompressed size.
Use the API to determine how much space cPanel will report for the email account:
uapi --user=username Email get_disk_usage user=user domain=example.com