As of DirectAdmin 1.39.4, a new feature will allow for the viewing of the disk usage breakdown with DA, similar to the output from the guide below.
If the disk usage is higher than you think it should be, or just want to know how DA is coming to the disk usage value, you can type:
cd /usr/local/directadmin
echo "action=tally&value=username&type=user" >> data/task.queue
./dataskq d800
This will run the tally for that account and dump out all the bits that are added together to come to the final value (system quota, email, database, etc.).