As above, I also use HS XML files as they are kind of "the standard" that artwork tends to be named against so as Pieter says, finding said assets is easier.
I also run
HyperSpin RomManager (plus others if needed) against roms as well as any asset folders as you can change the file extension to make sure everything matches and it also allows manual matching was well.
Its a bit tedious on large collections though.