Two questions; 1. I don't see any nodes in the cluster 2. Even though I specify the nodesubnetid's as private, EKS console tells me that cluster endpoint access is only public and all

Worker node traffic will leave your VPC to connect to the endpoint.

What am I doing wrong?

const cluster = new eks.Cluster(name, {
  name: clusterName,
  vpcId: vpc.vpcId,
  privateSubnetIds: vpc.privateSubnetIds,
  publicSubnetIds: vpc.publicSubnetIds,
  nodeSubnetIds: vpc.privateSubnetIds,
  instanceType: 't2.medium',
  desiredCapacity: 1,
  minSize: 1,
  maxSize: 1,
  createOidcProvider: true,
  skipDefaultNodeGroup: true,
})

const systemNodeGroup = new eks.NodeGroupV2(`${stack}`, {
  cluster: cluster,
  instanceType: 't2.medium',
  desiredCapacity: 1,
  minSize: 1,
  maxSize: 1,
  nodeSubnetIds: vpc.privateSubnetIds,
  instanceProfile: addInstanceProfile(),
})

It looks like you’re using the EKS component. In that case, you may need to add

endpointPrivateAccess: true

to enable private access to the cluster API endpoint. I’m not sure about the issue with the nodegroup, though.