I have made many changes the longer I work with the system. When I first started, titles were quite simple. As the system, as well as myself kept growing and expanding, I changed the workflow process pertaining to titles. I still give each note a unique identifier, but now find it benificial, similar to your mentioning, to make the title itself closely related to the actual atomic note. Yes, it is a bit shorter than the note, but very easily recognized by context.
Partiially answering your question pertaining to how I view my notes together, I have Index notes, or MOC’s. By doing the above mentioned, I get a wonderful overview. Everything is then all laid out easily showing the context of each note. At that point, if need be, I can open the note of interest to dig a bit further. Creating the indexes takes extra time, but also a great benefit. You purposely have to review…and that is a good thing!
The graph vlew for me, is kind of a mess. That is if viewed as a whole. The reason for this in my circumstance. I have way too many files and links. This happens because of my area of interest, Bible passages with notes pertaining the said passage.
I am still in the learning stage for the best way to handle a Personal Knowledge System and not unlike others mentions, evolving, growing, adapting as the growth happens.
Best of luck with your journey.