My father used to have a gigantic collection of index cards when he worked as a professor at a high school for librarians. We're talking about 100,000 cards or more. When he had to give a seminar session about topic X, he just selected a bunch of cards from his well-ordered, beautiful wooden storage boxes, fastened them with a rubber band, and took them for work. They contained references, small summaries, newspaper…
I think going plaintext might be the best way here. I wonder, though... I think writing something by hand gives a different feel for it. I don't know how to explain it. It's like your mind works better if you write by hand. So maybe an app, used with a stylus on a tablet or large-ish phone might be the best combination? It should then create folders and textfiles, and just store the text there. Which would require OC…
Handwriting definitely helps, but a lot of it in this system is done during reading (or just general life), which Ahrens calls "literature notes". Ahrens has a theory that handwriting forces paraphrasing, which he views as important to learning. Anyway, I handwrite all that, then there's a later stage of integrating the relevant info into the system.
For me, searchability and accessibility, plus backup (I write a ton on paper already and I'm a bit worried about losing notebooks) makes it worth the digital step.
Also, I suspect from initial usage that the Zettelkasten is what Krakauer calls a "complementary cognitive artifact": https://philosophicaldisquisitions.blogspot.com/2016/09/comp...
I.e., it makes you better at what you're trying to do even in the absence of the tool. To me, the main benefit of the system is that it encourages relational thinking.