Flathub is not enabled by default as of Whonix 17.1.1.5 - for VirtualBox - Point Release! but there are plans to enable Flathub by default in the next point release.
The development forum thread where this was notified is here:
Yes. I would assume you enabled it previously. Otherwise you would not be able to install anything.
If it’s installed, it’s installed. No further action required.