No, Tymeshift does not charge for all of your Zendesk users. You only need to pay for the Active Users on your Tymeshift account (we update the count of active users once a week).
Note that all of your Zendesk users are automatically imported into Tymeshift during the installation process. If you add more Zendesk users in the future, they'll automatically sync with your Tymeshift Agent List every 24 hours.
You can deactivate agents who won’t need Tymeshift or restrict Tymeshift to certain users. That way, only the agents who need to use Tymeshift will be able to access it.