In answer to the question in the title of your post, yes, you are supposed to answer questions about illegal drug use truthfully. Applicants for positions of public trust have an ethical obligation to answer relevant questions honestly. While your past drug use would presently preclude you from employment with, for example, the FBI (see current employment drug policy), it would not necessarily preclude you from holding a security clearance with another federal agency.

Keep in mind, however, that telling the truth is no guarantee that you will pass a polygraph examination, as many have learned the hard way. The "test" depends on trickery, not science, and while you may (and should) be completely honest with your polygrapher regarding relevant issues, your polygrapher will not be completely candid with you, as polygraph procedure depends on the polygrapher lying to and otherwise deceiving the person being "tested" about the nature of the procedure. Worse still, the "test" is inherently biased against the most truthful examinees. You'll find these deceptions exposed in Chapter 3 of The Lie Behind the Lie Detector. Chapter 4 provides suggestions for reducing the risk of a false positive outcome.