This issue has been resolved in version 6.0.1 and 6.4.0 of Syslog-ng Store Box (SSB). Please upgrade to either version to resolve this issue.
The correctly license count can be queried within the console/core-shell of the SSB either through physical access or via SSH by running the following command:
/opt/syslog-ng/sbin/syslog-ng-ctl show-license-info | egrep -i 'License-Type|Host-Limit|Currently-Used-Slots|Usage'
Alternatively, by running the following command the show-license-info will print the above information as well as every host that has used a license: