Thanks for your comprehension. I have no clues on how to troubleshoot this problem, since it happens randomly and doing unrelated actions. u/GL17CH suggested to check the SSD's health, this could have been an explanation, but its S.M.A.R.T. status reports it to be OK.

I am a long standing Apple user, and a senior software engineer, and I don't fully buy the degrading battery explanation. They got caught once and found a way around it, but there's more under the hood. I have seen iPhones slowed down since the 3G. It is such a regularly repeating pattern that it is mind blowing how they can get away with it. And the pattern is: a perfectly working and performant device degrades performance as soon as you reboot after the update. A battery does not degrade in the time of a reboot.