Protecting Drupal with htaccess

I noticed that if a site is downloaded using a program like HTTrack, the rule Options -Indexes does not affect directory viewing at all, since this program downloads part of the Drupal modules.

Moreover, HTTrack displays the installed modules, which is already a significant downside, as this program also allows partial downloading of module content, revealing library versions to potential attackers.. 

The question is, how can I use htaccess to at least prohibit the downloading of module content without compromising the functionality of the site itself?