Sometimes, the most efficient way to read a book is by taking notes (exceptions: biography, fiction, history book, etc.). And the most efficient way to take notes is using software.
If you use note-taking software, you can correct mistakes, insert new text, or delete some text on your notes easily. It’s easier to just press a few key on your keyboard, than to use an eraser or correction tape.
This is a very important benefit, since notes are made to be reread. And when you reread your notes, there are a lot of revisions that you can make to that note. I personally love to shorten the notes that I’ve written by removing superfluous words, since that makes subsequent rereading quicker.
If you use note-taking software, you can search for a keyword easily. Computers are better at searching words than humans.
This is a very important benefit if you’re an avid reader. Charlie Munger (from Berkshire Hathaway) are said to have a private room full of notes that he has taken. Imagine searching that room for a fact that’s written on a sheet of paper somewhere in the sea of paper there. If he used note-taking software, he won’t need that room (which can then be used for other purposes) and searching for a fact will be very painless (assuming he know the keywords).
As for the argument that writing with pen and paper can makes you memorize thing easier, let me share two anecdotes.
My Management Information System teacher in college insisted on this pen and paper method, and so I obey and create my weekly assignments with pen and paper. The result is that I always forget what I just write a few hours after I wrote it (or a few minutes after I wrote it, if I’m thinking about something else while writing my assignments in autopilot).
On the other hand, I use Evernote to take notes on the Refactoring book. The result is that I can recite the steps to duplicate data to separate business logic code from presentation code without checking my notes.
So, does your method of writing notes affect your memorization ability? In my opinion: nope. The things that affect my memorization are my presence of mind when reading something and how often do I use what I just read.
Since pen and paper doesn’t offer much benefit, I use software to take notes efficiently.