As the sibling says, org-mode easily delivers here. In ways that makes standard notebook environments somewhat frustrating with their limitations.

Examples:

You can reference data in a table of your page.

You can access the "session" of a code block in a repl. Useful for putting credentials or other sensitive data in.

You can copy from in a result or a code block with the same ease.

Any tags you have setup will jump as expected. Same for completions and documentation.

Arguably, the way images are referenced externally is better for post processing.

Finally, being able to source control the document easily is huge. Json is a terrible format. :(

Thank you all. It took me a while to get back to this thread and see your replies, but I very much appreciate them.

I'm convinced that you just pushed my over the limit to finally start learning org-mode.

And the examples sound lovely.

Org-mode can be pretty good for that kind of thing with many languages.

With many languages per notebook.