Search Files: Help path in Drupal scripts directory?

When you say "helper scripts" are you referring to the helper apps that search files uses to output the text of the various files?

If this is the case then no there is no reason that I know of why you wouldn't be functionally able to have those binaries/scripts in the {drupal_root}/script. I wouldn't advise it though. When you upgrade Drupal core it is suggested that you remove all the files except the {drupal_root}/sites directory. When Drupal core is upgraded by Drush this happens exactly. All files/directories except sites is removed and the new core Drupal code is put in place.

You would be better off placing the binaries/scripts for the helper apps in {drupal_root}/sites/all/libraries.

The auto-detection of helper apps will not work if the binaries/scripts are not located in a directory in the path.