The answer is right here: Tracking your numbers | Johnny•Decimal
Don’t worry, I kind of over-read it the first time, too. 
In short: Keep a central index.
That’s it, really.
You don’t have to and probably should not create empty folders/notes/whatever where you don’t need them. All your J.D numbers live in your index (and all of them probably live only there), along with a location (or several ones). And, yes, at least for me that means I (usually) create a new entry (anywhere) by creating it in the index first. So you’ll end up with gaps at the different locations. That normal.
Also it actually does not matter where you keep your index, I believe. Use what suits you best. I’ve personally experimented with Numbers and different outliners (especially OmniOutliner, MindNode and Zavala), but these days I just use a simple Markdown outline like this:
# 01.01 My J.D Index
## 10-19 Area
### 11 Category
- 11.01 Something
> Location(s): Things, Documents
- 11.02 Something else
> Localtion(s): Ulysses
etc. pp.
And, yes, the J.D index has its place the the J.D index, too. 
(Also see eg. My derivate of J.D (and P.A.R.A.) and Using an outliner for the index among other threads here.)
PS: Don’t diss Apple Notes—it has become quite capable nowadays! 