The entire Bill of Rights only exists to protect individuals from government actions. It does not exist to protect government from curious "citizens" or other interested parties. To attempt to use it in this way is wrong. People should have secrets from government; governments should have no secrets from the people.
What this means is that government secrets are not only wrong, but they are also illegal. Any ignored or rejected Freedom of Information Act request is a clear admission of wrongdoing. Any blacked out document that results from a FOI request is unambiguous evidence of guilt. Any government secret of any kind is illegal and a clear sign that the government is doing something wrong that it feels it needs to hide.
Now, you and I both know that government doesn't even bother looking for something to make its secrecy "legal", but it's good to remember that a government secret is a criminal act.