To flatten the file hierarchy for the lookup, especially if there are non-org files, you could try opening files using counsel-projectile (narrow a single flat list of file using regexes)
If a search-like interface works for you (such as counsel-grep-or-swiper) then the exact directory structure where you store your notes is less important (even a single [big] org file can work).
It might be easier to edit an Org tree than a directory tree.
If a search-like interface works for you (such as counsel-grep-or-swiper) then the exact directory structure where you store your notes is less important (even a single [big] org file can work).
It might be easier to edit an Org tree than a directory tree.