I have gone through the whole journey similar to you as well. It is so frustrating to keep searching for that perfect app only to find that every other app lacks something or the other. For the last year or so, I've settled on just plain markdown and the directory structure for hierarchy just like you.

I use my preferred editor (Emacs) to modify the files. I get to use all the functionality like key-bindings, search, version control. I push my notes to my self-hosted Forgejo instance (but it can be Github). Forgejo already has a web-interface the notes and links just work there.

On my laptop, I have mdbook configured to watch the directory and build the notes into static website. So if I just want to go through by notes or read something I can use that as well.

I tried finding solutions to take notes on my phone. But I realised that if its longer than a few lines than I prefer using my laptop anyways. I only ever read my notes on the phone. I've setup the same mdbook behind VPN so I can access it on my phone as well. If I ever want to modify notes on-the-go then I can use the Forgejo web interface as well.