specific htaccess in some sites on multisite i have several drupal sites running as multisite (same core + modules code), just moving to shared hosting 

Some sites should be kept password protected. (AuthType Basic) 

Is there a way to tell in .htaccess in drupal root that for certain HOSTNAME's
the password section should apply or at least a new .htaccess (in site subfolder) shall override
 .
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".