The option that you "checked" disables any and all downloads that go through the launcher. So all store content is disabled as well-- you would need to re-enable to option in order to get it back in your game, so if there's third-party CC you don't want, you'll have to find and uninstall it individually.
As for other items missing that read as installed, this is another issue that I'm starting to hear crop up, but there's no way for anyone to confirm whether or not it's oversight without knowing if it's specific objects in common. I know that some people said they were missing the fryer out of the new Fiesta set, and some have said they're missing the tablet. Could you tell me what item(s) you are missing?