feat(datastore): add remaining indexes on layers for alternative namespace usage query

mentioned in commit 14bf2262

mentioned in merge request gitlab-org/build/CNG!1249 (merged)

mentioned in merge request gitlab-com/gl-infra/k8s-workloads/gitlab-com!2455 (merged)

mentioned in merge request gitlab-org/charts/gitlab!2904 (merged)

mentioned in merge request omnibus-gitlab!6618 (merged)

mentioned in merge request gitlab-development-kit!2964 (merged)