One senior researcher I know, though an extremely early user of computers and Emacs, still uses basic paper notebooks for writing things down. The system is not searchable, not hyperlinked - but he still finds things almost effortlessly even though he hasn't been young for a long time.
So if the only habit that sticks is Apple notes - keep doing that. At least in my experience hyperlinking was never that useful, because the act of remembering what to hyperlink where was about as difficult as just remembering the what other notes exist - in which case, what do I need hyperlinking for? I also find hyperlinked text hard to read because you end up in Wikipedia style 3 pages deep hyperlink hell - a fun way to spend an afternoon, a terrible way to work and understand.
The act of physically writing things down commits the event to incidental memory. The more effort it took to concert all your neurons into outputting an action, the less easily it fades from your impression.
I find with physical objects I can better remember where it was spatially. I know that note was about 3/4 of the way through the green notebook, on the right-side of the spread, near the bottom of the page. Or something to that effect. I find the same thing with physical books over ebooks.
So if the only habit that sticks is Apple notes - keep doing that. At least in my experience hyperlinking was never that useful, because the act of remembering what to hyperlink where was about as difficult as just remembering the what other notes exist - in which case, what do I need hyperlinking for? I also find hyperlinked text hard to read because you end up in Wikipedia style 3 pages deep hyperlink hell - a fun way to spend an afternoon, a terrible way to work and understand.