How do I know Honeypot is working on my custom module form?
You can enable an option Log blocked form submissions on page admin/config/content/honeypot, set Honeypot time limit to, let's say, 30 seconds and try to submit your form faster than 30 seconds. Then check your log (admin/reports/dblog). You will see Honeypot log message if it worked.

And you probably should include some option in array:

  honeypot_add_form_protection($form, $form_state, array('honeypot', 'time_restriction'));



  Note that you can enable or disable either the honeypot field, or the time restriction on the form by including or not including the
  option in the array.
  (https://www.drupal.org/node/1232638)