I've updated the crd after it created the deployment and pods and services (adding configs, annotations and resources)but it seems the deployment is stuck where I started
Is there a way to update the deployment and pods besides removing the crd and destroying the existing configuration? 

Turns out the issue was the changed CRD had errors strimzi operator couldn't handle, following the logs of the operator pods, I've found the error and now it does update as expected.