In general you want to include the circuit breaker itself inside the zone of protection.
This means that CTs should be on the line side of a feeder breaker for standard instantaneous and overcurrent protection, as well as for transformer differential protection for the breaker feeding the primary of the transformer. For bus differential of a feeder breaker on the bus the CTs should be on the load side of the breaker, but for a main breaker feeding the bus the differential CTs should be on the line side.
For main breakers on the secondary of the transformer you will typically see CTs on the line and load side - the line side CTs are for instantaneous and overcurrent protection, and the load side CTs for transformer differential of the transformer that feeds the main.