specific htaccess in some sites on multisite
Apache does not support this.  You can use REWRITECOND to conditionally match rewrite rules, but there is no way to conditionally hide AuthType directives, except to separate the Drupal sites into different Drupal root folders.  Putting an .htaccess file in the sites/mysite folder won't work, because settings.php is read via php, not served up by the webserver.

Use Drupal features to protect your content.  If you turn off the "Access Content" permission for anonymous users, then a Drupal login will be required to view any page; all others will get "Access Denied".