It's not the EKS upgrade part that's a pain, it's the deprecated K8S resources that you mention. Layers of terraform, fluxcd, helm charts getting sifted through and upgraded before the EKS upgrade. You get all your clusters safely upgraded, and in the blink of an eye you have to do it all over again.
We address this by not using helm, and not using terraform for anything in the cluster. Kustomize doesn't do everything you'd want from a DRY perspective, but at least the output is pure YAML with no surprises.
We upgrade everything once a quarter. Usually takes about four hours per cluster. Occasionally we run into something that's deprecated and we lose another day, but not more than once a year.
Such a pity that helm makes this so awful. I suppose one could keep using it to package up complex deployments and tweak them with a values.yaml as long as you just use that to writeout kustomize and install that.
