I wrote an answer that might give you some insight here.

The missing piece of information that might give you some insight is that humoric medicine is a little misunderstood (and, in full disclosure, is something that I -- an actual historian of disease! -- did not understand when I was getting started in this subfield either, so when I say it's misunderstood I mean widely misunderstood).

The humors were understood to be the basis of the body's ability to accept or resist disease, which came from somewhere (no one was entirely sure where or how -- there were ideas that it had to do with bad air--miasmas--or that it could be contracted by inhaling the fumes of decaying bodies, and there were even some who theorized that it could be transmitted from sick people to healthy people (which, to the casual observer, would seem to be "contagion," but ... let's not go there).

So, simply put, the humors could be thought of in modern terms as "pre-existing conditions." If your humors were out of whack (scientific term), then you were more susceptible to catching disease, and that you might need to have things adjusted in order to return to health -- this could involve inducing vomiting, or bloodletting, or encouraging the patient to eat certain foods that were believed to simulate production of certain humors; the short version is that this wasn't entirely bogus. While bloodletting is, as we now know, an extremely dangerous procedure (although I think the stereotype of the medieval physician as resorting to bloodletting and "bringing out the leeches" is vastly oversimplified), the fact is that there was a fairly rich medieval pharmacological catalog consisting of what we'd now call homeopathic, herbal, or natural medicine, but using herbs and foods that actually have medicinal value for appropriate purposes.

The problem with the Black Death, as you surmise is nothing worked to treat it-- most care at that point was palliative, as it was pretty much known that if you contracted the plague you were going to die. And, even after pathological anatomical medicine became the standard, plague was still by and large untreatable until the discovery of antibiotics, which really didn't hit the mass market until after WWII.

In fact, the rapid onset of the disease in a geographic location contributed to theories that diseases were carried on miasmatic air, or could be triggered by atmospheric conditions, and/or that fumes from dead bodies could spread the illness. (Which makes sense to a point -- everyone had fleas; this is why markets where old clothing is sold were called 'flea markets' -- and, when people would come to pay their respects to a body laid out, the fleas would jump from the cooling dead body to the warm living one). This, unfortunately, also led to rumors that Jews or Romani were poisoning wells in some places.

So, all of which is to say, that, yes, it was known that humoric medicine didn't work against plague. But nothing else did, either.

The idea of humoural equilibrium or, in general, the influence of the internal humours on the general well-being of the patient was not the only mechanism of pathogenesis known to ancient and medieval European scholars. They largely used humoural theory to explain individual causes of chronic or sometimes acute conditions that were not transmitted to other, but they were aware of contagion and used it to explain the fast spread of a certain conditions among the population. Thus, from the Antiquity, medics understood a distinction between the exogeneous and endogenous conditions, i.e. those caused by some external influence and by internal problems. Of course, this influence was incomplete, and in many cases also incorrect, but it was there.

It can also be argued that in its most basic form, the humoural theory was never abolished or falsified, but rather refined and developed along the new discoveries in the fields of human anatomy and physiology. Using this approach, one can treat the ancient idea as a somewhat naive, simplistic but largely correct explanation of endogenous pathological conditions, i.e. those that are caused by the improper function of the internal organs that is caused by factors not related to external pathogens or environmental influences. This included most, if not all metabolic conditions. In many cases, the main cause of the pathological state is under- or overproduction of a specific chemical by internal organs, what influences body functions - an idea perfectly understandable by the ancient and medieval medics.

Possibly best known example of metabolic conditions is diabetes mellitus, caused (in a very simplified image) by inadequate production of insulin by the pancreas, what hinders proper digestion and usage of carbohydrates and results in e.g. elevated levels of blood sugar. Aretaeus of Cappadocia, a 3rd century scholar described the symptoms of this already well-known for centuries if relatively rare conditions and attributed it to the excess of cold and wet humours (or, conversely, lack of of warm and dry ones). In other words, it was a condition caused by excess or lack or some substances naturally existing in human body. This observation was spot-on, even though the detailed explanation and thus the recommendations was completely incorrect (as e.g. honey was considered 'warm' and thus would have been recommended by Areteaeus, although increase of the simple sugars intake in diabetes is not going to help, to say the least).

Now, when the Black Death (i.e. the first wave of plague) arrived in Europe in the late 1340s, people were very well acquainted with the idea of contagion and although they could not have precisely explain what it is caused by, they instinctively, and very correctly understood that some diseases can be transmitted between people and thus it is necessary to minimize contact with the sick. This was largely caused by the presence of leprosy that was largely thought to be impossible to fully cure before the advent of antibiotics in the early 20th century, but sequestration of the sick in leprozoria and leper colonies, as well as enforcement of measures minimizing direct and indirect contact (maintaining physical distance, wearing long clothes covering the entire body, sometimes complete with simple masks, destruction of clothes and items used by the sick) allowed to keep the leprosy to manageable levels. Thus, during first wave of plague, people were using similar measures, as evidenced by contemporary chroniclers. Soon after, local authorities also began to introduce quarantine. It wasn't as efficient as one could have suspected, because the main vector of plague transmission was zoonotic, i.e. the pathogen was largely transmitted by animals, and the idea that human might catch a deadly illness from a flea sting was something unusual for the medieval people.

This eventually led to a great fear and common association of plague with the divine punishment, as the illness seemed to be not caused by humour imbalance, as it could have affected people in perfect health almost overnight, it was apparently not just contagious (at least not to an extent understood by then) because the reduction of direct contact seemed to do a little to stop the disease, and it was unlikely to be caused by 'bad air', because it appeared all of a sudden without precedence (the last outbreak happened 800 years earlier, so for most people it was something completely new).

So, to sum it up, it can be said that the humoural theory was not applied to epidemics and contagious diseases in general, because when it was formed, scholars of the era were aware that contagion is a completely different process. Please note that theory of bodily humours was well known in the Eastern Roman Empire during the Justinianic Plague (bubonic plague) that occurred in 540s and it was elaborated on by Galen who personally witnessed the Antonine Plague (possibly smallpox) in the 160s.