When Change Auditor is installed all of the binaries for all available modules are also installed. This way, if you decide to add additional modules later, there are no changes required on the Change Auditor server other than adding additional licenses.
There is a "Hide Unlicensed Components" option found when clicking Action when on the Administration Tasks tab. This option will hide any unlicensed modules from the Auditing section of the Administration Tasks tab. This does not however remove the canned searches for any unlicensed modules as those searches are stored in the database.