>> If so, would a 404 reference in an htaccess file take precendent over the fact that the files still exist in the directory? <<
There is a misunderstanding here.
If the file still exists then it will be served with a "200 OK" reponse and the content indexed (unless you put a meta robots noindex tag on the page).
If there is a 301 redirect for that URL declared in the .htaccess file then that file can not in fact be accessed. The redirect is served first, and the browser then requests the new URL that it was told to ask for.
The server can only give a 404 response if the requested file is NOT found on the server.
The ErrorDocument directive tells the server to show the content of the named file, instead of the standard "Error 404 - Page not Found" message that is built in to the system.