Having read most of what has gone back & forth on this thread, I'm inclined to agree with Tim that I don't like excessive nesting of subdirectories (and I am an IDE user myself - PHPStorm).
Option 2 - mod/xxx/classes/aaa/bbb_ccc.php seems to me to be the best version for plugins - enough nesting to prevent excessive numbers of files in one directory, without the opposite problem of having to navigate through large numbers of subdirectories to find what you are looking for.
I'm not quite sure how that maps onto core libraries (and whether the same solution is needed for both plugins and core code).
I notice that the discussion has also moved on to namespaces, but that is something I can't comment on at all, as I have no experience of working with namespaces ...