Typical skeptical disclaimer: I don't say that I know for sure chi doesn't exist, or that accupuncture doesn't work. I do know that neither has been proven, that other explanations for the effects some attribute to chi/accupuncture do exist and are sufficient. So if real evidence ever does show up, well then, my current skepticism is still justified, but I'll accept the evidence as it is. I don't have a horse in this race, chi's a cool idea, but it seems an arbitrary construct to me. I don't see the difference between it and the Force emitted by the midichlorians (or however George Lucas spells them). Dismissing one because it was invented more recently than the other seems unfair.
Your observation that "scientific studies on human health" are difficult (quotes correct here!) is absolutely true, it's why there's been years of research regarding some of the alternative medicine world's claims - especially regarding accupuncture, which has good anecdotal evidence in its support - even though there's been little success finding an effect that can't be otherwise explained. It's important to be careful and critical about accepting poorly supported results. To belabor a point: the scientific method can be used to test the efficacy of treatments such as accupuncture. There does not exist a body of successful experiments that demonstrate a clear effect, or show a mechanism by which it works. There are several studies that fail to disprove any effect. I suppose that's something. As you say, it's difficult to isolate one factor when we're talking about health studies, but there don't seem to be any that are strongly indicative in accupuncture's favor, and there doesn't seem to be a large number that are slightly indicative either. So it can be regarded at best as an unproven treatment. For a treatment that has been around for so long, to have the best evidence in its support being anecdotal or even weirder being that it's been around a long time, so there must be something to it, should lead one to be skeptical at best.