The disk management tools on the Security Management server object only delete the current logs in the active $FWDIR/log directy.
The Security Management server has had an in-place upgrade from a previous version in the past.
For example: If the Security Management server was running R76 previous to an upgrade to R77.x, the logs from the /opt/CPsuite-R76/fw1/log directory will not automatically be deleted and will continue to consume space on the partition.