There's certainly a risk that an individual will rely too much on AI, to the detriment of their ability to understand things. However, I think there are obvious counter-measures. For example, requiring that the student can explain every single intermediate step and every single figure in detail.

A two-hour thesis defense isn't enough to uncover this, but a 40-hour deep probing examination by an AI might be. And the thesis committee gets a "highlight reel" of all the places the student fell short.

The general pattern is: "Suppose we change nothing but add extensive use of AI, look how everything falls apart." When in reality, science and education are complex adaptive systems that will change as much as needed to absorb the impact of AI.