Are there two identical .htaccess files in a Drupal installation?
There are actually 1+n .htaccess files in any given Drupal directory, where n is the number of working sites:


In the Drupal root
One for each site's files directory


The contents of the files directory .htaccess file is the following:

SetHandler Drupal_Security_Do_Not_Remove_See_SA_2006_006
Options None
Options +FollowSymLinks


This was done as part of a security update to Drupal 4.6.x and 4.7.x, and has been there ever since. The relevant security advisory, SA-2006-006, explains why:


  Certain -- alas, typical -- configurations of Apache allows execution of carefully named arbitrary scripts in the files directory. Drupal now will attempt to automatically create a .htaccess file in your "files" directory to protect you. This line references SA_2006_006 to lead Apache administrators to this announcement.


Thus it's not advised that you replace or remove that file.