There are 2 different thoughts here I think. If using GitOps in Kubernetes, then application and set up (Pods) aren’t associated with Nodes (EC2). And both can be torn down and rebuilt without state issues. When state is required, then PVCs and Stateful Sets come into play.

For managed services like S3 and RDS, there are other GitOps tools like Crossplane.io which you can use for similar GitOps management. But the paradigm shift might also be that you add GitOps config to perform regular backups, and also add config to ensure that if it is being recreated, it restores from a backup.