I wanted to write the same thing. have the notes app do the notes thing and handle encryption elsewhere.
as to apps, I suggest QOwnNotes. it’s markdown, highly configurable so you can make it minimalistic AF, stores notes in invidual files and folders. it also has a bunch functionality like syncing to nexctcolud and such, but I’d advise against it, just use it as a notes editor. you don’t have to selfhost anything, make it use the e.g. Documents/Notes folder and you can use syncthing to securely replicate it to other devices.
first off, if you plan to scan the storage for bad “sectors”, that’s gonna take eons if the disk is of any considerable size. what’s more likely is you running the SMART self-test and that will work over any medium.
the cables absolutely can and do cause corruption, whether it’s plain SATA-SATA cables or the USB-SATA with their own controller on it; however, if you don’t have reason to suspect this particular cable/adapter is faulty, it’s not a worry vector per se.
I deployed RocketChat on two different client installations (didn’t check the licensing you’re mentioning, I’ll have to look into that) and I run a Prosody instance (XMPP) on my own; tried Matrix for a short while and ran away from that mess as fast as I could. anyhow, although the messengers work without any significant issues or downtime, the amount of flak I get from non-tech normies about the client apps is staggering.
the apps just aren’t up to current UX standards. they’re used to Twitter and iMessage and Telegram quality UX, and getting used to these PoC-quality apps - both on mobile and desktop - makes them “feel icky”. I’ve had to intervene on a number of occasions when some of them transferred their business-related comms to other platforms because they just can’t/won’t get used to these apps.