Having some familiarity with the concept, I would say Scrivener is way more suitable to that technique than Scapple. 
The concept of having a “box of index cards” so to speak, doesn’t pair well I don’t think with a tool that helps us write out thoughts for what could be described as a single “card”. I.e. rather than a “card” or a text file, as the case may be, we have a spatial environment to put one sentence here, another there, and maybe now and then draw lines between them to represent heavier relationships or logical lines of movement.
Sure, you could try and push it beyond that, have very long notes and put thousands of them into one board, but you’re going to run into all kinds of problems in my experience. One of the main reasons people write in to Scapple tech support with issues (from heavy lag to crashing) is because they are putting massive amounts of information into a program that was designed to replace napkin scribblings. And by massive, I really don’t mean all that much, a few hundred notes can bring it to its knees. It just wasn’t optimised for that, at the levels of drawing or storage. So, in my understanding of a traditional Zettelkasten, where everything goes in is one of its core philosophies, smaller scale software like Scapple seems immediately inept to me.
As you say, Scrivener does notes—it is a box of cards, and one designed to scale into the millions of words across tens of thousands of entries. Each entry in the binder can be an entry in the box—or it can go beyond that and represent one entry through several child items, it’s flexible. More importantly to what you’re saying though, it does connections. You may not see them like lines on a chalkboard, but as far as I’m aware that’s not really what Zettelkasten technique is about anyway—it is more about the powers of association through common referencing of entry identifiers in a way that parallels how tags are often used. It’s fundamentally text based. That’s not to mean one couldn’t try to find something that somehow visualises text-based connectivity among thousands of notes, but to me it seems like that could get messy no matter how you slice it… but see the list below for one program that might be the right choice for you.
In Scrivener, here are some topics that can help with establishing and managing connectivity between notes:
- Every section in Chapter 10. But specifically…
- §10.1, Linking Documents Together. The first half of section is going to be vital reading, if you intend to design a Scrivener project to work as an archive. Some of the not-so-obvious tools in there can be game changing, like turning on the
[[link syntax detection]]function. - §10.3, Project and Document Bookmarks, with more emphasis on the Document Bookmarks aspect. The former has its uses, but for creating a networked cluster of data within the binder, its the ability to list relationships in the sidebar that matters. Lots of programs let you create hyperlinks in the text, through one mechanism or another, but few let you store lists of general relationships—and I’m aware of no other tool that lets you view and edit the contents of a link list in the sidebar of the thing you’re working on. Almost everything requires you to navigate, leaving your context or cluttering your workspace with windows. That one concept alone can be revolutionary to how you work.
- The other two sections, on Metadata and Collections may come in handy or not. They are not principles that apply directly to Zettelkasten techniques verbatim, but I would say that is largely because those ideas were designed for index cards in a box. But I think the notion of using Keywords as binding mechanisms, or custom metadata to highlight important pieces of information (like the document ID number), and collections to help organise relational clusters of notes (so you don’t have to keep searching for an ID over and over) are all extremely compatible with the idea, in the same way that using a text editor is compatible, instead of a pen and card stock. Collections are also the “left side” companion to Document Bookmarks. You can create a collection and drag a bookmark list over into it, which takes the listing and makes it global, as well as extending all powers of the binder sidebar to it: i.e. everything the main editors can do.
- I’d say a cherry picking of topics in Chapter 12 would be useful to know about for taking Scrivener beyond its stock model approach. Effective and efficient navigation and window layout understanding will help you broaden your workflow beyond one or two items at a time. Learning how to fine tune the project window to work toward a specific workflow can mean the difference between plodding around painfully through huge lists with the mouse, and having every thought you’ve ever had under your fingertips in seconds.
Of course there are many other aspects of Scrivener that can make it go from a “book writing tool” to a “note taking tool”. I’ve used it extensively for that purpose, with million+ words of data. The fundamental principles of a systematic approach to archival design, combined with a program that can tap into that design and illuminate it are quite extraordinary. The difference between Scrivener and most of the other tools out there for note taking is that Scrivener can become a note taking tool whereas most of the rest are already that. It may seem a liability, but that would neglect the fact that it got to that point through its flexible feature set—the implication being that it can better mould itself and adapt to your system, as a specific system, than most special purpose tools would. With the latter you’ve got to hope lightning strikes twice: once in your own brain for how you prefer to work, and the second time in the brain of a developer that coincidentally made a tool exactly how you work.
Anyway, it’s a big topic, but here are some further programs to think about, even if just for inspiration:
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Tinderbox (macOS-only): I’d say it sits somewhere in between Scapple and Scrivener in some regards. It has Scrivener’s outline-based approach and supreme flexibility, but at the same time is very visual, and is deeply invested in the notions of linking things together, being based upon established hypertext principles. There is even a Zettelkasten starter file which is quite detailed in its implementation. As I mentioned above, if I were to think of attempting an idea like this in a visual metaphor, where connectivity is something that can be seen, rather than listed or programmatic, then Tinderbox would be my choice, without much deliberation. The main reason to hesitate is the same reason for Scapple: they both use a single document storage architecture, and that effectively limits how much data you can put into a single file, and breaking things into discrete files breaks the philosophy of this approach.
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The Archive: you’re probably aware of the website as well, but if not, there are a few years worth of reading in there.
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Zettlr: another program built specifically for the process. As with The Archive, it is file system based, which to me is almost a mandatory requirement. Data cannot scale without either a database or a file-per-note approach, and the latter is in most cases superior as you can ditch the software at any time with almost no loss of data. One thing that I like about Zettlr’s approach is that even though it has a good array of settings to adapt itself to how you work, it does not have an overwhelming latitude in how it can be used on a daily basis. The workflow is pretty simple, and does just about all it needs to.
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EagleFiler (macOS only): before adopting Scrivener to this purpose, this was for a little under a decade my main tool of choice for this type of information management. Back then PKM had no spiffy jargon or theory built up around it (nor that abbreviation), and I don’t think anyone but very specific types of geeks had ever heard of Niklas Luhmann. So there wasn’t much by way of software built around the idea, and today it might feel a bit lacking given that. But I mention it to pay homage to a program that served me well for a long time—and even if it lacks the bells and whistles you might expect for this workflow, there is something to be said for keeping the software as simple as possible. It stifles procrastination and tinkering, and keeps you doing what you came to it to do, with little fuss. Plus, it’s use of the native filesystem is a big bonus in my opinion.
For those Mac users looking for more raw power and flexibility in a program like this, look no further than DevonThink.
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The file system. Yeah, that’s it, just .md/.txt files in a simple directory layout (the simpler the better). You can’t get much closer than a box of index cards than that—but don’t be fooled into thinking no software equals no technology. There has been a few good threads on this: this one is quite old and describes some formative ideas on the concept, with some more recent thoughts later in that thread, after years of refinement. Here is another post on organising information for a file system based approach, and overall another good thread to read.