The Zabbix API is really great, but there're a few issues with it worth knowing about:

• Audit: Many Zabbix API operations aren't registered in the Zabbix audit log, which can be accessed by going to Administration | Audit. That can make it really complicated to find out who made a particular change and when.

• Validation: Unfortunately, the API validation leaves a lot to be desired. For example, using the API, one could change a host to a proxy or vice versa, or even set the host status value to a completely bogus value, making that host disappear from the frontend, although no new host with that name could be created. Be very, very careful with the possibility of sending incorrect data to the Zabbix API. It might complain about that data, or it might just silently accept it and make some silly changes.
• Error messages: Similarly, even when validating input data, the error messages aren't always that helpful. Sometimes, they'll tell you exactly what's wrong, but you may also get incorrect parameters for a long JSON input string.
• Performance: The Zabbix API's performance can be extremely bad for some operations. For example, modifying items for a template that's linked to a large number of hosts, or linking many hosts to a template, might be impossible to perform. While some of these operations could be split up, for example, linking the template to a few hundred hosts at a time, in some cases, we would have to fall back to doing direct SQL queries.
• Missing functionality: Although the Zabbix API allows us to control most of the Zabbix configuration, there're still some missing areas. By now, that mostly concerns things found in the Administration | General section. Once such functionality is implemented, it'll finally be possible for the Zabbix frontend to stop performing direct database queries, and the API will allow writing custom frontends without ever resorting to direct database access.