In the exact same boat. Strongly prefer writing notes for many reasons but no easy search really sucks. I currently use Notion mainly as a personal wiki and to-do tracker. Each day gets a new page where I jot down notes and tasks in a loosely structured format. I have found Notion's search to be very useful when trying to remember how or why I did something months ago. However, I still keep a physical, unruled, bound sketchbook for when I want to draw out class relationships, diagrams, etc - i.e anything that is much easier to describe on paper than with text alone. I usually don't need to actually "use" these diagrams - they're more a tool for working out and untangling an issue that eventually gets translated into code. Even with "paper-like" iPad screen protectors, I still strongly prefer writing on paper. So I have not found a way I like to combine Notion and physical writing yet.

But this post has me thinking about separation of concerns. Maybe I should stick to using Notion for anything that I want to search later and use the notebook for the aforementioned drafting and as a work-specific journal. While I haven't tried it much, I believe there's value in "brain-dumping" your day in a simple fashion similar to a diary. A therapist may advise you to deeply introspect on your overall state for that day, which I do think is a valuable tool, but may cause some inertia as a hard requirement for a "work-specific diary". Writing daily events in a simple fashion alongside some optionally additional, also simple, notes could help sort of "flush your mental buffer" of grand-scheme unimportant day-to-day information and help remember more important information. Sort of in the vein of Sherlock Holmes concept of his "mental attic" in the sense that you want to take care of removing/prevent clutter and instead keep track of what's useful to you.

The most important stuff is generally stuff to be memorized, which takes longer than just copying it once but means it's always there when you need it. Even if you only partially memorize it, you remember "oh yeah, there is that one idea..." And the tricks to memorizing are basically forms of "monkey-see-monkey-do". Involve more muscles and sensory info. Add short spacing periods so that the idea lingers. Place it spatially. Writing definitely helps for this since it's slower, physically involving, and you can style it with different formatting and stationary. Real media also works better for these aspects of writing and drawing because the hand-eye coordination is more connected; once it has to go through the computer there is digital goop in the way making it a little laggy, a little aliased or oversmoothed. You go to do something and get interrupted by everything else the computer does. So I do end up with use-once paper just for the purpose of training my brain better.

If I need to organize my paper I stick it in a manila file, label the file, and put a binder clip on. Then it has both spatial position and index. If it gets bigger than that we can grow to a file bin, hanging-file cabinet, etc. But nearly everyone's essential personal or project data is going to max out at one or two cabinets. Above that you are most likely becoming an archivist for other people's data and probably getting away from the task at hand.

For the stuff that is "linking together existing sources", where you can start consuming a vast amount of external data, I have taken to stuffing it in a spreadsheet. Spreadsheet cells are versatile enough for nearly any discrete-informational task and you can organize them into cheat sheets pretty easily. But they aren't so structured that you have to spend a lot of time preparing the structure either, which a lot of dedicated note systems seem to fall into: again, you have to set cutoffs wherever you start turning into an archivist. It can make sense to professionalize it as part of an organization, just not for yourself.