I made a mockup of what I'm thinking on.
The first image is the current setup, using an actual record from my database.

- current.jpg (55.51 KiB) Viewed 19029 times
This is my proposal. In the Notes field I identified the headers or folders with "# " (it can be anything else, maybe a choice?) and the notestream view interprets them as headers with a different size and color coding:

- proposed-expanded.jpg (49.71 KiB) Viewed 19029 times
That's the default view. The user can collapse headers by clicking on the arrow (or pressing the right arrow), and this is what it'll look like:

- proposed-collapsed.jpg (31.74 KiB) Viewed 19029 times
The collapsed header shows that it has 4 notecards in it, similar to the Mail.app interface to message threads.
Two notes: 1) the notecard sizes are still fixed, the only difference is that headers have two lines; 2) To me the color coding and size would be a great benefit to easily identify the structure of the notes. The collapse/expand feature may be useful, may be not.
I hope it makes better sense now!
Thanks for your time.