The pen is your friend.
I think you should use what works best for your class, but I agree that pen and paper has advantages in some contexts. My Civ Pro prof was very straight-forward. He lectured straight bll. I liked using my laptop for that class because I can type much faster than I write, and his lectures were literally packed with information that was relevant to the exam. Also, Civ Pro isn't really an abstract, conceptual course.
On the other hand, I used paper notes for Property because future interests were much easier to draw and the prof used the pure Socratic method so lengthy notes weren't necessary.
As for One Note, I have a friend who swears by it. She says it's a lot more fun than using Word. I'm very proficient with Word, have a ton of macros set up and prefer to use that.