"I don’t see how it helps the humanities and other sciences to teach skills which are never used." - I can offer an unusual counter here, you're assuming the knowledge will never be used, or that we should avoid teaching things that are unlikely to be used. Were this the case, the field of graph theory would have ceased to exist long before it became useful in mapping - indeed Bool's algebra would never have led to the foundations of computer science and the machines we are using today.
"How is it a threat to education when someone uses a new tool intelligently, so they can pass academic education exams?" - Allow me to offer you the choice of two doctors, one of whome passed using AI, and the other passed a more traditional assessment. Which doctor would you choose and why? Surely the latter, since they would have also passed with AI, but the one without AI might not have passed the more traditional route due to a lack of knowledge. It isn't a threat to education, it's adding further uncertainty as to the outcome of such an education (both doctors might have the same skill levels, but there is more room for doubt in the first case).
"Wether their education was this or that way has no effect on the advancement of science in general, because these people don’t do science in their career." - I strongly disagree! In an environment where knowledge for the sake of knowledge is not prised, a lie is more easy plant and nurture (take for example the antivax movement). Such people can be an active hinderence to the progress of knowledge - their misconceptions creating false leads and creating an environment that distrusts such sciences (we're predisposed to distrust what we do not understand).