Have you checked the SMART values of your drives? Do they give you a reason for your concerns?
Anyhow, you should never be in a position where you need to worry about drive failure. If the data is important, back it up separatly. If it isn't, well, don't sweat it then.
Also not a fan about the closed source thing, but I like about Obsidian that it's all just markdown. If I ever need to ditch it, I can keep and use my existing files as they are.
Would this also be possible with Zettlr or Logseq?
I don't understand - you want a layer to hide database internals but also a web app that "is only the db itself"?