The WHMCS Firewall module scanner performs two roles.
First, it inventories and tracks all modules installed in your WHMCS. If a module id added or removed then you will receive an alert.
Second, the module scanner has a Whitelist feature that allows you to whitelist specific modules from the WHMCS Firewall rules.
*The WHMCS modules scanner works with file integrity monitoring feature so if a module is not removed but the files are edited inside it then you will still receive an alert.