It works because normally you do most of the thinking in your head, so the few occasions you are doing deep thinking using paper and pen, you have the disciplin

It works because normally you do most of the thinking in your head, so the few occasions you are doing deep thinking using paper and pen, you have the discipline and care to only write what is important and keep the rest in your head. If you do everything on paper, it will start being not much different than doing everything directly on computer because you will be writing everything and you will lose that abstraction and care.