Até onde eu sei, o próprio OSSEC não exclui logs. Veja a documentação
Where are OSSEC’s logs stored?¶
On OSSEC server and local installs there are several classes of OSSEC logs. There are the logs created by the OSSEC daemons, the log messages from the agents, and the alerts. Agent installs do not have logs from other agents or alerts, but do have logs created by the OSSEC processes.
All logs are stored in subdirectories of /var/ossec/logs. OSSEC’s log messages are stored in /var/ossec/logs/ossec.log.
Log messages from the agents are not stored by default. After analysis they are deleted unless the option is included in the manager’s ossec.conf. If set all log messages sent to the manager are stored in /var/ossec/logs/archives/archives.log and rotated daily.
Alerts are stored in /var/ossec/logs/alerts/alerts.log, and rotated daily.
Você pode usar o logrotate para girar os logs do ossec, mas a pasta /var/ossec/queue/diff
é outra história.
Você pode excluir os arquivos com segurança e manter a funcionalidade do OSSEC, mas perderá os relatórios de diferenças.