Zabbix supports Linux agent auto-registration and it’s a well documented process in the Zabbix manual. However, it’s not really straightforward to mass provision Zabbix agents on hundreds of servers if you want to have Zabbix agent <-> Zabbix server communication encrypted. At least not without some form of additional scripted step in your installation process. For large deployments I usually use Ansible, although this article just briefly covers that part and I’ll mostly focus on how to make sure your agents get registered for encrypted communication.
Zabbix 3.0 introduced a major new feature – encryption between Zabbix components. If you’d like to add a new host with encryption enabled, you would go to the documentation of the host.create method… and be surprised. It says nothing about the encryption at all. You might continue to the host object page, but that wouldn’t have anything on encryption either.