I would love to have a close integration with Zotero, but perhaps that is out of scope for a BibTeX plugin. But I will write down my thoughts about it anyway 
If you look at the Roam Zotero-plugin, this offers a really great integration between Roam (another note-taking app) an Zotero. It uses the Zotero API and of course that enables many features that are not possible just with BibTeX.
But I love @dimi-huer suggestions to have a closer integration with a reference manager, similar to the Obsidian plugin that is based on BibTeX as well. (I think for many Joplin users that is Zotero as it is the most popular Open Source reference manager. I would love to get the results of your questionnaire @xUser5000). I think two basic features are essential for that:
- Usage of Zotero URIs for references in Joplin, no DOIs or similar.
- Create a note a an individual reference. But this shouldnt be an automatic process for every paper/book etc. in my BibTeX file, because that can be far to many. These notes should be created via a menu, directly linked to one Reference and have a specific template which includes the metadata and space for notes.
The second feature could be done manually by the user as well, especially with the coming templates plugin, but transferring all the metadata would take a lot of time. Another advantage is, that you can not accidentally create two notes for the same reference. For my workflow it is also beneficial that a Joplin notes "represents" one reference because I am using backlinks and a knowledge graph, which is much easier to realize with links between Joplin notes.