I'm trying to build up a system within a private VPC and I need some containers to communicate between them. Its important to say that for now I'm not using any kind of internet connection, so no NAT gateways, for example, to access others AWS services, like SES or ECR, I'm using VPC endpoints.
But there aren't a VPC endpoint for AWS Discovery Service. There is any way around that, or I will have to enable a NAT gateway to use AWS Discovery Service?
AWS Discovery Service is not the correct service for the problem you are trying to solve. AWS Discovery Service is for helping large enterprises prepare on-premise environments for a migration to AWS.
You want to use either AWS App Mesh, or AWS Cloud Map. It looks like AWS App Mesh supports VPC endpoints. At this time Cloud Map apparently does not support VPC endpoints. Cloud Map uses Route53 Private Hosted Zones, so address lookups would work perfectly fine without an Internet connection, but I think you would have to have a NAT Gateway to update any endpoint information in Cloud Map.