Technically, this only shows instances that has a community that at least 1 user has subscribed to, or that has users that subscribed to a community on your instance.
If no traffic has gone between them (nobody subscribed either direction), it won't show up there.
Yes, in which case they're not strictly federated with them. If you click "All" in that instance, no posts from the missing instance will show up. The "All" list shows all instances that the instance is federated with.
They're not explicitly defederated, necessarily, but they're not federated, not until a user subscribes.
I'm not sure how it works in either direction. Like, if a user from one instance subscribes to another, but no users from the other instance subscribes to the first, then the federation will maybe only be one way.