How should PhD Students/Researchers take notes?
In this article, "The Pen is Mightier than the Keyboard," the researchers tested this very issue.  They found that taking notes with pen and paper is more effective... but, that was because students who typed their notes were copying lectures verbatim whereas students who took notes by hand were taking in the information and then writing it in their own words (thus processing the info at a deeper level).

So, the key is the way you process the information, not necessarily the method you use to take notes. But, at the same time, it is noteworthy (no pun intended) that longhand notes tends to lead to that deeper level of processing more so than does taking notes digitally.

Personally, I'm all about taking notes longhand, and I print out articles that are important to me/my work.