I agree with you 100% plus, I'd like to take it up a notch by saying that Pure FP evangelists are the sole reason why Scala is not widely used.
Also, it is not seldom that you hear them say "It took me n years to fully grok the _whatever FP concept_". Or Martin Odersky doesn't get the _whatever FP concept_.
So how do they expect the majority of sw engineers will use/adopt those principles if the guy who invented Scala "does not get it" and even themselves took so much time to "get it"...???
I use org-mode (in spacemacs), folder synchronized on some cloud, private notes GPG encrypted. For me it's more than perfect. I always find what I am looking for immediately, org-mode is useful in lots of other use cases, emacs has been around for a long time and I trust will stay for the rest of my life...
I second org-mode. Previously I was using OneNote but that is limited to Windows, and on Linux I need to be always online to use the web interface.
To add one more use case: I was thinking of creating flash cards and came across org-dribble which provides the entire functionality of creating and revising flash cards using Supermemo method.
When it comes to note-taking and organising, org-mode is an excellent choice.