The first one shouldn't be used as a directory. The second one, can be used.
The reason the first one can't, is because it is just the search directory of one instance. Each instance knows/shows a community only AFTER some user has indexed it manually by putting the full url of that federated community in the search bar and submitted it. Only after this, does lemmy.directory will be able to show it.
The admin from lemmy.directory actually stated that his instance tries to fetch all communities from everywhere in order to build a directory, it's not meant as an actual, general instance.
The above are great ways to find communities l, and if you struggle to subscribe once finding one (it can sometimes be surprisingly confusing), check out https://lemmy.blahaj.zone/comment/39208.
Ok I have a dumb question. Is [email protected] supposed to have the same content as [email protected]? Or are those two similarly names, but separate things with potentially differnt content?
They're different communities with the same name, because community names don't have to be unique between different instances. I get that subscribing to two different communities with the same theme is annoying when you could save time and subscribe to one, but having backup communities is a blessing when the instance shuts down or mods start power tripping. A "multireddit" feature that can combine multiple communities into one subscription feed would keep subscribing convenient without forcing only one community to exist per topic.