Trickery and deception when it comes to medicine and personal health are never fair game. I think there's definitely a difference between police telling a suspect "we know you did it" (when they don't actually know) and a doctor telling a patient "take this and you'll feel better" (when the drug actually does nothing).

Also, polygraphs are a little bit more functional than homeopathic medicine: a polygraph can not only induce nervousness, but can also notice it in some cases (even if the nervousness may not be concerned around a particular question and may not necessarily indicate deception and even if there are false positives). This helps create a feedback loop which makes it more powerful than a pure placebo (e.g. a "lie detector machine" you hook someone up to which isn't powered on at all and does literally nothing).