I assume that you have HTTP scanning or protocol filtering disabled as well. Note that doing so exposes the computer to Internet-borne threats.
As for suppressing notifications about malfunctioning Antiphishing protection, make sure that you have the following modules in ERA installed:
Translation support module 1625 (20170906)
Configuration module 1526.2 (20170811)
With these modules, you should have 3 options to disable notifications related to Antiphishing protection in the Application statuses setup: paused, disabled, non-functional.