Suppose the following sentence:
"Aren't the headers not covered by copyright?"
Is this sentence correct?
Yes, it's correct. But if you get at yes or no answer, I bet you won't know how to interpret it.
If you do away with the contraction, your sentence is:
This means what you are trying to confirm is that the headers are not covered.
This is confusing, but it isn't a mistake unless you're trying to confirm the opposite. If you don't mean to have a double negative, you have the choice of including the negative before or after 'the headers', so instead use either
In either case, you aren't opening up the respondent to a yes or no answer. If you want a clear answer to your question, you're better off saying:
If you want to get across the fact that you were under the impression that headers are not covered by copyright, then you should say: