Insider trading investigations generally work by looking for unusual trading patterns, especially prior to large market movements. So any NSA employee who's had substantial gains from classified information in his possession would already have been investigated by the NSA.
Security clearances, especially TS ones, come with very elaborate requirements that I'm certain would include a requirement to disclose that you're being investigated by the SEC. Even if it doesn't (or the employee decides not to disclose it), I'd be surprised if there wasn't some exchange of data between the SEC and the clearance authorities. Since trading in the public markets based on classified information constitutes a leak, you wouldn't keep your clearance for long.
Security clearances, especially TS ones, come with very elaborate requirements that I'm certain would include a requirement to disclose that you're being investigated by the SEC. Even if it doesn't (or the employee decides not to disclose it), I'd be surprised if there wasn't some exchange of data between the SEC and the clearance authorities. Since trading in the public markets based on classified information constitutes a leak, you wouldn't keep your clearance for long.