I think that if your admitted drug usage did not preclude you from holding a TS/SCI clearance, then it is unlikely to preclude you from holding a security clearance with the CIA.

Apart from an ethical obligation to answer relevant questions truthfully, it would be incredibly stupid to falsely deny behavior that one has previously admitted to on a form SF86. The investigative file associated with your current clearance will indeed be available to the CIA, and while your past drug use may not be disqualifying, being caught lying about it most certainly will be (and rightly so).

As for the polygraph process, it is true that complete candor is not always the smartest action. The "test" is predicated on the secret assumption that everyone -- even people the CIA would want to hire -- will be less than completely honest when answering the so-called "control" questions. Perversely, the more candidly one answers these questions, and as a consequence feels less stress when answering them, the more likely one is to fail.

Because of the unreliability of polygraphy (which, as the National Academy of Sciences confirms, is without scientific basis), even truth-tellers may wish to consider using polygraph countermeasures to protect against the risk of a false positive outcome. The information provided in Chapters 3 & 4 of The Lie Behind the Lie Detector will help you to make an informed decision in this regard.

Also, be aware that depending on the position for which you are applying, you may be ambushed with some very personal questions. See the public statement of "No Such Author" for examples.