Thanks for bringing this up! I use something similar to the Zettelkasten method described in How to Take Smart Notes.
If you’re not aware of it, you should check out The Archive, and the community forums they have there.
I currently use Drafts for pervasive capture, and as a “operational memory” area, while using The Archive for longer-term, static, conceptual knowledge. I’ve tried various ways of combining these things into one, but have increasingly seen the value in stratifying different kinds of knowledge storage.
I can see some uses for linking in Drafts, and might give it a spin, but there is a problem there for long-term information upkeep. If your links depend on any kind of app-specific or proprietary formats, they will all eventually break. If you’re trying to create a collected, life-long knowledge-base, then you don’t want this.
The system I’ve adopted for linking is what the makers of The Archive use. Basically just put IDs everywhere. Specifically, timestamps. This works across paper journals, Drafts, notes, and documents of all kinds. Mine look like this:
201911222025 Include in filename.txt
Include in body of a Draft: 201911222025
A later [[201911222025]] reference or backlink
An alternative #201911222025 reference or backlink
Any app which recognizes the double-bracket search format can make this really fast. Or you can manually execute the search yourself. I haven’t yet tried making a script for Drafts to recognize these links, but that might be worth trying.