How to enable VPC Endpoint setting about multiple private subnet per AZ

You can deploy one SSM endpoint in one of the subnets in the same AZ, as described in https://docs.aws.amazon.com/vpc/latest/privatelink/concepts.html#architecture-diagram

Note that clients in the other private subnet would still be able to talk to SSM through the endpoint. And by default, each interface endpoint can support a bandwidth of up to 10 Gbps per Availability Zone and automatically scales up to 100 Gbps. A bit more details are available here: https://docs.aws.amazon.com/vpc/latest/privatelink/create-interface-endpoint.html#considerations-interface-endpoints

You can specify more than one subnet in different Availability Zones to help ensure that your interface endpoint is resilient to Availability Zone failures.