Not all requests to cPanel/WHM from the cPanel module are logged to the module log. One that was an issue recently is that when using API Tokens, the permissions must allow "Everything" otherwise fetching a list of Reseller ACLs when creating a Package with an Account Type of "Reseller" does not work and it is not logged. cPanel/WHM actually returns an unauthorized response, but you wouldn't know that by looking in the logs.
That, and any other requests that are not logged should be logged in addition.