HyperCard would be an interesting one. Is the linked stack an actual tool or just a presentation/essay with ideas on howyou might use HyperCard for it? (I forgot to hit post here, but it gave me time to just go try it, the stack is just an essay, but with HyperText added. If you click a link in the text it plays a noise and displays an illustration to the left.)
When I was noveling on my 1400, 6100, and 180 in 2016 (or 2017? I need to go back and figure out which) what I ended up doing was having a separate notes file. I mostly pantsed the actual plot, save for a pitch I'd put together as a part of another project, so I had a copy of the pitch, a record of what happened in short/summary form, then character and location names I'd used.
Either a single app that can have multiple documents open or a single app whose documents can be relatively large would probably be the easiest way to do that. I don't happen to know of any other structured info-bases specifically for fiction of novel writing, the way you'd use, say,
Scrivener on a modern computer.
If you have a suitable system 7 machine, you might combine an outliner with a word processor, and just consider location and character notes to be part of their own top-level outline at the start or end of your plot notes. I tried this, Claris Impact, which works on 68k but is fairly heavy. (So, Impact and MacWrite Pro and Resolve wouldn't really run at the same time on, say, the PB180).
I ended up reverting to a single MacWrite Pro doc, a simpletext notes file, and both a simpletext word count record and a Resolve file to be updated primarily on the higher end computers (anything with enough RAM to have MWP, SimpleText and Resolve open at once.)
I said it before and I'll say it again: I heavily recommend against writing a novel in Frame/FrameMaker. That's probably even more inappropriate a tool for fiction writing (I'll argue: for writing copy in general) as just writing a story directly into XPress or PageMaker/inDesign. If you have enough RAM to do that, you
probably have enough RAM to run System 7 and MWP+simpletext or Impact.
The other-other option is to just use the Mac for your text processing for the novel itself and use an ipad or a paper notebook for the other notes. As a NaNo thing this year I gave my wrimos little gift packs that had 100-packs of index cards in a little zip-closed bag, a pen and a sticker, the intent being that you might write notes about particular things on the cards and either post them on a wall/board or keep them with them in the pouch. (It's a technique I've been meaning to try, but I always design myself out of wall space in any home I have instantly.)