Application Control is a free service
Application Control is now a free FortiGuard service and the database for Application Control signatures is separate from the IPS database. However, Botnet Application signatures are still part of the IPS signature database since these are more closely related with security issues and less about application detection.
With the release of FortiOS 5.6.1, Application Control signature database information is displayed under on the System > FortiGuardpage in the FortiCare section. And the Botnet category is no longer available when searching the Application Signatures list.
IPS / Application Control logging performance
There is a major boost to Application Control and IPS when logging is enabled. With the latest changes, the performance difference with or without logging enabled is negligible.