The documentation says that only pods that are managed by a Replication Controller will be restarted after a Kubernetes cluster update on Google Container Engine.
What about the pods that are managed by a Deployment?
In this case the language is too precise. Any pods that are managed by a controller (Replication Controller, Replica Set, Daemon Set, Deployment, etc) will be restarted. The warning is for folks that have created Pods without a corresponding controller. Because nodes are replaced with new nodes (rather than upgraded in place), Pods without a controller ensuring that they remain running will just disappear.