All packages sent to your client from WMS will be installed fine. WMS controls the Write Filter. If WF is enabled, WMS will disable it, reboot, install, reboot and enable it again.
If WF is disabled, WMS will only install the packages.
For virus pattern files I would recommend excluding a folder within the WF and store pattern files there.
However, most AV programs also store information about pattern files in the registry and this would fail, of course then.
Therefore, best practice would be to use a Next-gen AV program, which does not rely on pattern files anymore. A very good solution is available from Crowdstrike.