1. It's always super helpful to write things down. Taking notes from what I read/learn is a great way to verify that I understand it. It sharpens my thinking.
2. However, maintaining the "second brain" is a lot work. It's not only about "linking" together notes. You also need to maintain some consistency between them. I ended up spending a lot of time thinking about the structure instead of actually thinking about the content.
3. Most of my notes/thoughts fall into two categories: (1) Either they are critical for something I'm actively working on or (2) it's just loose concepts that I'm toying with. For (1) I immediately end up playing with it in code — which is far more concrete and tangible than notes. And for (2) it was rarely important to retain the knowledge accurately many weeks/months later.
What I've ended up with is taking a lot of notes, but I hardly focus on organizing them.