Kong's Prometheus plugin not returning all metrics

You shouldn’t be using Ingress Controller and dbless configuration at the same time.
The DB-less configuration (dblessConfig) will be replaced by Kong Ingress Controller.

Please create a CRD KongPlugin with name and plugin set to Prometheus.

Have a look at the following guide:
https://github.com/Kong/kubernetes-ingress-controller/blob/master/docs/guides/prometheus-grafana.md