Sorry, I don’t really have anything to offer, other than it is a live issue for me. I keep paper journals/notebooks - I find handwriting on paper with a nice pen helps me think and retain information (and gets me away from the distractions of technology). In some pastoral situations sitting with a notebook seems less intrusive than an iPad.
I use a referencing system (e.g., NB1/23 = page 23 in notebook 1). I want to refer back to my notes (and often do), but indexing is an issue.
Jonathan Edwards kept an index in each of his paper notebooks. If he continued a topic later, he would include a reference at the bottom of the previous journal article, so providing a ‘trail’ through his notes. Not so different to a Zettelkasten, just a couple of centuries earlier.
I write note references in my Bible margins, which effectively acts as an index to my notes. However, the challenge is for everything else, not scripture related. I need to create my own index.
The only way I can think is to have a long file exactly as you suggest which acts as the index. It might be possible just to reference the first item for each topic, and in your notebook reference any subsequent items. Having a master index across and separate from notebooks makes sense, in that a topic may appear in several notebooks. An alternative to your approach might be to include all references together e.g.,
Sanctuary of the Great Gods #greece #travel 132 794 1044 1045
The benefits of journalling #pkm #journals 133 401 1211