Explanation of pear's include path, and why Drush cr clears it?
Pear has no connection to this. The error message displays the include path value in brackets for debugging purpose. You can check the value as follows:

drush ev 'print get_include_path();'


In your case the PHP is trying to include the file from this location and emits the error as it fails.
/var/www/d8site/modules/custom/somemodule/somemodule.module

My guess the file still presents in Drupal registry because the module wasn't uninstalled properly. Check out this guide to fix it. https://www.drupal.org/node/2487215