Drush is always scanning the whole drupal directory? Every time i run a drush command the command returns after 40s. (or more if time consuming operation like cache clean or so)

After strace the command i realized that drush is scanning my whole drupal directory. I have mounted via nfs an storage with thousands of Files which are accessed by an own module and i think there is no need for drush to scan these files on every run. 
Is there an option to exclude a path ?

my files are in drupal_root/sites/default/files/my_module/nodes/nid/

Greetings Robert
There might be something wrong with your module... You say there are more than a thousand files scanned but are they placed in your module's directory ?

Drush is not supposed to scan your sites/default/files folder for instance or any other data folder you might have set. As a  best practice you should not place data in your module's path (obvious... isn't it ?). If you have done so, you should think about moving them somewhere else.

When executed, Drush scans all activated modules path (along with a few others such as sites/all/drush) for .drush.inc files. This is the expected behavior and that might cause your slow script execution.