As a term used in distance bicycling, "bonk" is used in various ways, mostly because good bicyclists aren't always up on their biochemistry, but my understanding of the term is that "bonk" is used to refer to the situation when the human body runs out of glycogen.

As a brief biochemical guide, the human body has three stores of fuels: free blood sugar, which lasts for about ten minutes, glycogen, stored in the liver and muscle tissue, which can last for around an hour of exercise, and stores of fat throughout the body that can last for days or weeks. When cycling, the body quickly runs out of sugar, but glycogen in the liver and muscle is broken up for glucose both to provide energy to the muscles and to run other body processes: including given glucose to the brain, which prefers glucose for fuel, and a lot of it. After that fuel is exhausted, the muscles will start burning fatty acids, protein or pretty much anything available for fuel. For the most part, this isn't a problem for the muscles: they aren't too discriminating. As a byproduct of the breakdown of fatty acids, molecules called ketone bodies are produced. The brain can survive by metabolizing ketone bodies, but doing so puts it on alert from what it takes to be a state of starvation. This leads to a series of metabolic changes that can be both harmful (it can be detrimental to thinking and reaction times) and helpful (for some people, including me, it involves some type of "cyclists high").

Although some training regimens actively seek for a "bonk", because it means that the body will be burning fat, I find it detrimental for several reasons: first, operating a bicycle can be a hazardous activity, and a brain that isn't fully alert is a brain that doesn't notice the potholes in the road until it is too late. Secondly, once I reach the point of running out of glycogen, I will become ravenously hungry, and remain so for sometimes a day or two afterwards. By eating regularly, I never reach the point of wanting to overeat. Thirdly, feeling weak and hungry is not a way to make cycling a regular, fun activity, which is the best way to build it up as a regular, healthy habit.

I am not the largest expert on either bicycling or biochemistry, and people who know more about both of these might have different opinions. The biochemical picture is, of course, also much more complicated than I described here. However, as someone who knows some biochemistry and has completed a century, I would suggest keeping a constant supply of glucose on any long rides.

Notice, also, that I am using the term "bonk" for a fairly limited phenomena: there are other sources of fatigue from cycling, that I don't usually see described as a "bonk".