
It isn’t. We know huge amounts about nutrition. You could (and people do) fill libraries with what we know about nutrition.
Whatever makes you think we know less about nutrition than about any other field of science?
You had best start first by explaining why you believe that medical science knows so little about nutrition? Compared to what does it know so little? And how did you do this comparison?

Doctors know a huge amount of very specific information about nutrition. If you ask about the metabolic fate of fructose or the physiological effects of protein deprivation the average doctor will be able to provide you with enough information tot fill a small book.
Can you provide any evidence at all that this is true?
As have a number of astrophysics questions, a number of biochemistry questions, a number of civil engineering questions, a number of ecology questions, a number of…
If this is your standard of “knowing so little” then we “know so little” about literally every field of study.
For the same reason that astrophysics can’t answer why the Voyager probes are slowing down and why ecology can’t answer why or even if bee populations are declining.
It’s because the differences, if they exist art all, are relatively tiny compared to the background fluctuations in any possible control in natural system. As such, it’s almost impossible to separate out any putative effects form random variation.
This isn’t especially true of nutrition compared to any other field of science. All the low hanging fruit have been plucked. All the questions that were amenable to easy study have already answered. All we have left are, of course, questions that are difficult to answer.
In many cases the questions are ones, like your sugar question, where we aren’t even sure that there *is *a question. There may not *be *a difference between different types of sugar. Even if there is, the effect is so tiny compared to genetics, exercise, age, the rest of the diet and so forth that it isn’t showing up reliably in controlled studies. Every field of study has these types of questions and, of course, always will. This isn’t evidence of “knowing so little”. It’s just evidence when you’ve resolved all the big, easy-to-study issues you will be left with little hard-to-detect issues.
Others, like your salt question, are not even a question but an issue of ever-increasing accuracy. All nutritionists agree that one pound of salt per day is injurious. All agree that 1 mg per day is not. So we actually do have agreement on how much is injurious. You just aren’t satisfied with the accuracy off the answer. And if the answer fell between 100mg and 5 mg, would you be satisfied then? Why? Or if it fell between 1mg and 1.00001mg? You are simply setting an arbitrary level of accuracy that you require and claiming that we know “so little” because the current state of knowledge doesn’t have enough decimal places. But once again every field of study has these. The speed of light or the circumference of the Earth, for example, aren’t known to an infinite number of decimal places. Do you take this to mean that we know “so little” about relativity or geology?