How do I make DirectAdmin suspend based on disk usage?
By deafult, disk usage is not a candidate to trigger account suspensions.
This is for a few reasons, one being the fact that the system quota will enforce the upper limit anyway (for user created files) and also that they won't be able to login to delete files if they're suspended.
If you still want to suspend user who go over their usage limit, you can do so by using this feature:
If you're wondering why the system quotas would allow more than 100% usage, the answer is that they don't.
DirectAdmin counts more than just system quotas in it's usage total.
Things like mysql, webmail data, etc are all included in the totals hence the number can exceed 100%.