Ivan,
It sounds like we're in a very similar boat. I work in academics, and I've recently started using TiddlyWiki for its strengths in networked thought and open source nature. I know very little about coding, so I've had many of the same questions you're asking. Currently, I'm using a single-file wiki (not a node version with individual files), and it's working very well for me at this point.
My primary use case is academic research. In specific collecting notes on research and then connecting and compiling those notes in a way that allows me to outline, draft, and eventually write up new scholarship. That means tons of notes and specifically a mountain of PDFs. I have found TiddlyWiki to be excellent at connecting, compiling, outlining, and even drafting. I then export my finished articles to another tool for printing or publishing.
I believe your notes are more future-proof in a TiddlyWiki than they are in most other note-taking tools. It's been mentioned in other comments so far, but an HTML file is essentially a text file than can be human readable even if the unthinkable happened and there was a wholesale shift away from browsers reading HTML to render websites. Futhermore, it really seems unthinkable for HTML and browsers that read it to go away. From my limited understanding they appear to be the backbone of the (frontend of the) internet. I use a Chromebook personally and more and more it seems computers are really just gateways to connect us to the internet to do everything. So, I think we're safe with HTML documents for a very long time.
As for PDFs, this is a real concern you need to consider. It's been said above already, but you don't want to store the PDFs in the wiki itself. I have several thousand notes in my single-file wiki currently, and it runs just fine. But, none of those notes are embedded images and files, and I did that on purpose based on the wise counsel of this group. Instead, I've chosen to use a reference manager to house my PDF files and link to them or reference them by citation. It works well for me, and it keeps the wiki running smooth. I use
Paperpile as my reference manager. It indexes all of my PDF articles and any books or other sources I use in my research. It also has it's own PDF annotation tools, so I read and annotate my PDFs in Paperpile and then export any notes I want to make more "permanent" in my research to TiddlyWiki. I upload the PDF to Paperpile and it stores it in my Google Drive, so I still maintain control of the actual file. This also creates a shareable link to the PDF itself. You can link to the file that way in TiddlyWiki.
In addition, I use two plugins that facilitate this process. The first is the bibtex plugin you can find in the main plugin library for TiddlyWiki. It allows you to export a bibtex (bibliography file) from your reference manager and upload it to TiddlyWiki in a way that parses out all of the sources and creates a reference tiddler for every book or article. Then, I use the
refnotes plugin to easily cite these sources in my other notes. The refnotes plugin works in the background to compile a works cited for projects I'm drafting and allows me to easily cite references on my notes so I know where they originated.
Paperpile is not the only reference manager out there.
Zotero and
Mendeley are probably the two most popular, and they share most of this functionality I just mentioned. But I really like the combined ability of using a good reference manager with the power of TiddlyWiki.
Hope that helps you think through options some. I've spent the better part of this year thinking through all of this myself, and this is where I landed.
Good luck!