hey, welcome to the forum
What's your opinion on using OCR for the PDFs and highlight the text of significance by creating a new linked note?
This way you could build a robust linked searchable knowledge base.
Plugins to achieve that
Plugin: offline OCR (extract text from images, pdf, videos, etc)
Other than that, there may be developed a plugin that would retrive "named destinations" links from a PDF. Those destination links could be used to navigate inside a PDF (url-to-file/file.pdf#nameddest=dest3) and additionally linked within the note structure of Joplin.