Fix code quality: Add accessCheck to entity queries and inject service

atul_ghate → made their first commit to this issue’s fork.

The code changes do not follow Drupal coding standards.

Also NW for the removal of a valid comment with a pointless "Use the injected module handler service to check module existence", which basically describes the inserted line, but doesn't really say WHY the line is there.

The other funny part is that the patch does a lot to remove a call to \Drupal calls, but proceeds to then replace that with a \Drupal call in another class.