No no no, not at all!
Firstly, Magnussen’s mental powers work very differently to Sherlock’s. While Sherlock practices the science of deduction, reading between the lines and making leaps which are usually, but not always, correct, Magnussen works purely on solid data. As a blackmailer, he cannot afford to be wrong - then he would lose his power over his victims. He does not take that risk by making leaps. Instead, he just collects data and commits it to memory. At the stage in which we see the characters’ pressure points listed on screen, Magnussen has never observed a situation in which Sherlock has been vulnerable and John has shown how much of a pressure point he of course is for him. He has seen John vulnerable and Sherlock exhibiting his weakness for him, but not vice versa. Had Magnussen read them after Sherlock was shot and John was clearly very frightened and upset, I have no doubt in my mind that ‘Sherlock Holmes’ would’ve been listed as one of John’s pressure points.
Secondly, at the end of the episode, where Magnussen explains his chain of pressure points, this still doesn’t negate the fact that Sherlock clearly is a pressure point of John’s. Magnussen does not have a means of blackmailing John or Sherlock, but he DOES have a means of blackmailing Mary, and so the chain holds. Of course, John is bound to be concerned about Mary, particularly since she is carrying his child, but he also cares about Sherlock, the chain just wouldn’t work that way. It’s not John he wants to get at, it’s Mycroft, so John has to feel threatened, so that Sherlock in turn feels threatened, so that Mycroft in turn feels threatened. The only way to do that, again, is through Mary.