I capitalize if a technical designation.
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The difference between "It was a secret document" and "It was a Secret document" is that the latter is very clear about technical classification (whereas former is not). Though I wouldn't write latter sentence for that reason: "The document was only classified Secret" is clearer.
I also avoid using the term Top Secret unless it is really the technical designation. Term is often over-used (but to be sure, classification status is too!) as generic when it is supposed to be specific category.
