It looks like the issue you found of missing communities may have been because those communities hadn't been subscribed to by anyone on this instance previously, and were therefore unknown to the instance. There is an automated process that periodically subscribes to top communities on other instances, but newer, niche communities will have to be manually searched for before they begin to federate with this instance, per the Lemmy 'Getting Started' guide:
These previous ways will only show communities that are already known to the instance. Especially if you joined a small or inactive Lemmy instance, there will be few communities to discover. You can find more communities by browsing different Lemmy instances, or using the Lemmy Community Browser. When you found a community that you want to follow, enter its URL (e.g. https://feddit.de/c/main) or the identifier (e.g. [email protected]) into the search field of your own Lemmy instance. Lemmy will then fetch the community from its original instance, and allow you to interact with it. The same method also works to fetch users, posts or comments from other instances.
This also means that content is federated from the point of the first local subscription (it won't pull in older posts unless they're pinned). This is why you're only seeing pinned posts for [email protected] and [email protected] as there have been no new posts in either community for a month or more.
As for posts being marked as 'hidden' for a new user, that's not something I've come across before. Is it happening at all on established communities or only new (to LS) ones? We updated to a new version of Lemmy a couple of days after you joined, so if it was a bug hopefully it has been squashed.
Sorry for not responding sooner - this one flew under my radar.