There’s the classic “you can’t add too much water to the reactor” where “can’t” can mean you are physically incapable of adding too much water, and therefore should add a lot, or “can’t” can mean you must not add to much water.

Yes, but that’s not so much a problem with the language but more an issue of sentence construction. A big part of good communication in any language is anticipating that sort of ambiguity and adding context or rephrasing to remove it if required.

‘Can’t’ is really too passive to use if it really is ‘must not’ for anything serious, so while the sentence could work either way in spoken communication (because you can convey enough context with tone of voice and emphasis to imply which sense you mean), it would still not be a great choice of words if you mean the second sense.

"Can't" isn't even the slightest bit passive. But a person who is telling others how to communicate well will always use technical terms with the wrong meaning.

In this case a negative imperative is what you should be using. Moreover, since it's a life-or-death matter, we need to carefully explain ourselves. "Do not add too much water to the reactor. If you add too much water, the reactor could explode. The reactor should never contain more than 1000 litres of water. If it is overfilled, immediately follow the steps in 3.4.1 to perform an emergency evacuation." By being careful in our follow up, we reduce the risk of any misunderstanding. We cannot prevent a person from misunderstanding, but at least they are more likely to realise they have misunderstood something and seek clarification.

"Must not" is reasonably well-understood by native speakers of English, but it is confusing to non-native speakers because even though "must"="have to", the negations have different meanings. It is no use being technically correct if the person whose responsibility it is thinks you said "you don't have to add too much water to the reactor". The prevalence of "must" also varies throughout the native-speaking world.

Especially in german where “You must not“ reads very similar to “Du musst nicht“

Which means “You don’t have to”

“Yo must” could be correctly translated to “Du musst” though...

That's an ambiguous question in native English too and could only be fully, precisely understood from context.

While I would interpret the sentence from only the context you provided in the way that you describe, I would characterize the question as unclear. A military chain of command would definitely phrase the question more like "Mr. President, can you confirm you are giving us the order to launch the nukes? Please present your confirmation code."

But I understand what you mean about negations having opposite meanings in (spoken) English (where context is clearer). I consider that kind of negation and answer to be sloppy written grammar and something to avoid in written English.

French and German, at least, have handy words (si and doch respectively) that just serve to contradict a negative question.

I think doch and ihr (plural you) really need to be in English. I sometimes use yous for ihr, but unfortunately no equivalent for doch yet.

That's because はい/いいえ doesn't mean yes/no, it means correct/incorrect. Though the yes/no response to negative questions is also different in American and British English.

Saying hai is "correct" is misleading in its own way: no English-speaking child will say "correct" to "Would you want some ice cream?", but "hai" is what a Japanese kid would say.