Not all subdirectories are included, though. Subdirectories whose names do not start with a letter or digit are excluded. Subdirectories named RCS or CVS are excluded. Also, a subdirectory which contains a file named `.nosearch' is excluded. You can use these methods to prevent certain subdirectories from being searched.
Emacs finds these subdirectories and adds them to load-path when it starts up. While it would be cleaner to find the subdirectories each time Emacs loads a file, that would be much slower.
This feature is an incompatible change. If you have stored some Emacs Lisp files in a subdirectory of the site-lisp directory specifically to prevent them from being used, you will need to rename the subdirectory to start with a non-alphanumeric character, or create a `.nosearch' file in it, in order to continue to achieve the desired results.