Top level directory files like readme.txt are served by apache
As I understood - you want to hide the txt files on the root direcroty (e.g. Changlog.txt) from prying eyes, therefore you can search Drupal.org for that question (its there..), and you'll see 3 types of solutions:
1. Leave those file as they are ( I don't like that option)
2. Just delete those files
3. Hide them using the site's .htaccess (My favorite option)