It is certainly true that typing out notes is generally a bad idea. I have and can take notes on a computer while basically unconscious and getting no benefit from them; transcription is easier than and a distinct activity from taking notes.
However, with pen computing, the computer becomes a very useful note taking tool. I can write out my notes in OneNote while recording the lecture. If I miss something or want clarification, I can go back and listen to the lecture, linked up by time with the notes I took.
I can go back and search my notes - they are useful for quickly reviewing a topic I may have studied in the past.
I like color coding my notes. I can write in any color, recolor after the fact if I want a different structure, and generally add multiple channels of cues for my studying.
Digital ink & paper have potential to replace physical notes without the negatives of typing.