On admin/modules, I can see the version of Drupal core modules, and third-party modules.
For third-party modules, Drupal will show the version only if it finds the necessary information in the .info.yml file of the module. In the case of the Honeypot module, this is what Drupal finds.
# Information added by Drupal.org packaging script on 2016-03-11
Without that, Drupal doesn't show the module version. For example, this is what Drupal shows for my custom module, which is not hosted on drupal.org.
If you are using modules that aren't hosted on drupal.org, or you don't use Drush to download the modules, you will not see the module version. This also happens if you clone the module repository with Git instead of downloading the module archive from drupal.org.