It may not have anything to do with fear of spying. Drug use is something that a) most people have done, and b) are least willing to admit to. While some of us may shy away from telling people of our sock fetish or whatever, admitting to drug use has real and far-reaching consequences.
So in other words, getting you to admit to drug use would likely be a reasonable representation that they have ascertained "the whole truth" from you.
Also if the operator can't see an alteration in the graphs, he can think that the subject has been "inmune" to the machine and try to break him "manually" like in the linked article or like arockwell's wife. The drugs would be used because, as the interviewer himself said in the linked article: "everybody have done drugs some time", so it's a good guess, even if it's "most people" instead of "everybody".
The issues that government agencies have with drugs are (1) blackmail potential and (2) risk behavior.
To maintain a drug habit, one usually needs a relationship with a dealer, and drug dealers (in addition to being criminals) are generally pretty awful people. So, if you're a regular illegal drug user, there's someone out there who is (a) committing a serious crime, (b) probably of bad moral character, and (c) knows that you've done something illegal. Although it's extremely unlikely that a drug dealer is going to blackmail his clients into revealing state secrets, putting oneself into such a position is taken as a sign of bad judgment.
The second issue with drug use (as pertains to the psychedelics, most of which are not illegal, e.g. salvia) is the risk attitude it shows. Drug use is taken as an indicator for how a person handles low-frequency risks with very high loss potential. Since no one who hasn't used psychedelics can understand their subjective effects and risks, a person who takes a mind-altering drug is undertaking at least an epistemic risk of blowing out his mind. There's obviously a valid philosophical debate regarding how the risks of drug use compare to those of other pleasurable activities (sex, skydiving) and, frankly, I don't think psychedelic drug use is worse, from a cost/benefit perspective, than a host of "normal", socially acceptable human behaviors. However, the psychological risk inherent in drug use is taken by government agencies to be fairly singular: people who die in skydiving accidents don't present a risk of revealing state secrets or creating image problems for government agencies.
The government security clearance process seems to be very focused on recreational drug use history.