A direct call to the agent can be a personal call therefore it should logically not appear in the stats of the UCCX. Only the agent's work related calls, therefore coming from the helpdesk queue, should be incremented, otherwise the stats will not be so reliable.
You cannot measure calls which are not ICM routed calls. For, you to monitor this, you shall need to check the CDR on the CCM or have accounting configured on voice GW.