I tend to write with more intent when using paper because I know that editing is not really possible. Accessibility is also much more limited on paper. However, I think of my devices and PKM software as a second brain where I just offload information knowing it can be accessed anywhere and anytime. P.S. From TokyoU’s Department of Basic Science (in an allegedly predatory journal).
I’ve never noticed memory differences based on how I made a note. I have, however, noticed that the act of making notes helps me understand something (which isn’t necessarily the same as recall) and writing on paper works best for me.