What kind of law of custom is there in a health matter?!

The question is whether this is really about health. After all, some argue that it is not health in the ordinary sense (spiritual dangers and the like). If it were ordinary health, then once there is no health concern, there would indeed be no reason to observe it (see the Tur regarding legumes).

What is the explanation, in general, for medicine having entered into Jewish law? If something is dangerous, then it is forbidden because it is dangerous, so why is there any need, beyond that, to prohibit it?
(Regarding meat and fish, as far as I recall the Magen Avraham already writes about this that nature has changed.)

That is not precise. See here:

הלכה ומציאות – מהי מומחיות הלכתית

“Not health”—do you mean that it does not cause leprosy but something else (that is, that something else is something else), or do you mean that leprosy itself is really something spiritual?
If it is option B, then our entire ability to issue halakhic rulings has been blocked off, because maybe there are really hidden explanations that have nothing to do with what is written.

I did not mean to ask what this has to do with Jewish law, but rather that the prohibition should not be specific; it should include all risks at level X, and from that point on one should ask a doctor whether such a thing is a risk at level X or below that.
And therefore there is no prohibition of meat and fish, but a prohibition on danger; and then one should examine on the merits whether it is dangerous or not.
After all, among many of the God-fearing one hears the claim that even though it is not forbidden, still, when the reason has lapsed the enactment does not lapse. And about that I ask: why in the world would the Sages enact a prohibition on meat with fish? At most they should say that meat with fish falls into category X and is therefore forbidden. And once it has become clear that this is not so, or that nature has changed, what sense is there in keeping the prohibition? From the outset this was not a prohibition on meat and fish as an object in itself, but on danger, and this is not dangerous.

Yishai,
The approach of hidden reasons is well known, and I do not agree with it. But that is when we are dealing with a law whose reason is clear. There, the supposition that perhaps there is some hidden reason is unreasonable, and there is no logic in being concerned about it. But in the case of mixing meat and fish, there is no clear reason. The Sages speak about danger, and it is not clear whether this means ordinary physical danger or some kind of spiritual danger. So here it is not necessarily connected to the general approach of hidden reasons. Maybe yes and maybe no, and that is why I wrote only that one can be uncertain about it.

Itai,
But it is impossible to establish a sharp level X that is halakhically forbidden, and it is also very hard to determine the level of medical risk. Has anyone determined what level of risk on Yom Kippur permits eating? Is there any doctor who will tell you what the level of risk is in this or that illness if you do not eat? There is no way to do this, neither on the halakhic side nor on the medical side. Therefore, the Sages sometimes establish a prohibition on a certain act that in their view falls into the category of forbidden risk. And therefore it is possible to see meat and fish as a prohibition and not only as a danger. Though, as I said, it is certainly also reasonable to see it only as a danger, and then it would not be binding if it becomes clear that there is no danger.