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 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.