It sounds like the issue was that the two primary female characters in TNG were the doctor and the counselor. Whenever the two of them talked professionally it was probably going to be about a patient, and there was a good chance the patient would be male. For VOY, when the captain and chief engineer communicate professionally it would usually be about a piece of machinery, which would of course not be male.
Well she was obviously making an excuse to be there and everyone in the room knew it. Id guess the security clearance was something like manually verifying his identity and registering him with the computer as part of the command staff. This would normally be the sort of boring paperwork the computer or a lower level security person does off screen, but she wanted an excuse to be there and the clearance was technically something she was responsible for.