How to make notes on journal readings – necessary, or emergent skill?
I work in the field of biological sciences, specifically computational biology and am a newly graduated PhD. I say this, because I may make statements which are field specific.


  Is note-taking an essential skill? 


Partly no. While I do not consider note-taking to be an essential skill (because I have never been able to take good notes), now I lend much higher import to organisational skills and tools for the job. 

For example, I have never been much of a note taker, but I have good contextual memory. So for most of my PhD, I invested in a reference manager, where I can quickly access my papers. I read papers end-to-end in the beginning because everything was very new at the time. But, for the better part of my PhD I have never read a paper end-to-end, I start from 1 paper and within the next 2 hours, I will have skimmed through another 5. 

Afterwards, for the rest of the day(s) I will keep on thinking about what I had read, what it means, how does it conflict or fit with previous literature and how it relates to my work. These are all my mental notes.

If I need to go back to the paper, I can open up the reference manager and I can locate the paper to read the paragraphs of interest once again. There are many cases where I may not remember the author, title or journal and year of the paper (rarely happens). In such cases, I fallback on other papers which cited the paper of interest and which I may have happened across the same time. 


  Would it develop naturally if I 'needed' it?


In my experience, my current process works the best for me. Note taking did not help me when I needed it (under-grad, masters). But, the above process which I developed during my masters works the best for me. The only time I take notes, is when I need to visualise some ideas. Even then, they are not notes, but rather abstract drawings. 


  How can I rectify this moving forward? It's gotten to the point where my academic future literally seems to hinge on this silly issue, because it takes me so long to make notes on content that I fall behind, all the while feeling that I am struggling to understand


I would suggest that you make your peace with the idea that you (like me) cannot suitably apply note-taking procedures that have been developed by other people. Once you do this, you can try to tailor a procedure that works best for you. This should also help you boost your confidence. This, I think is key towards increasing your productivity.