Offtopic, but I use org mode for my notes files (both general and technical), and I've never really figured out how to use it effectively. My pre-org notes file was just a giant text file with entries delimited by manually-entered '--------------' lines. I stuck a topic in each entry for searchability and then the rest was freeform text. It worked pretty well. org mode gives me more power, but it's getting a little u…
I hear you on isearching. To support multiple files you could look at ag.el for fast cross-file search (although not incremental like isearch).
Alternately you can use :tags: to add a different dimension of information by which things can be grouped. org-agenda can then be used to see items by tag (also since they are just text you can search them in a buffer). I use org-agenda in 'F'ollow mode whereby a second buffer shows the selected agenda item in its original context. It helps visualize where things are while navigating.
The new hotness, ala org-roam, is bidirectional linking with tiny files. That would probably be a pain to migrate to, and isn't really aligned with your free-form model. But it might be the way to scale over the long term.