Unfortunately in my experience unless your building a local development environment, in which everything can be started and stopped at once, and it all runs on the same machine, container linking is effectively useless.
I think Docker Swarm has fixing this on the roadmap, but for now I think Kubernetes is the only thing to take into account the fact you'll probably want to have more than one node in a Docket cluster.
Please refer to https://github.com/docker/docker/issues/9983. The Networking concepts are completely revamped using this proposal. Links are being replaced with concepts like Network and endpoints. State Distribution and Service Discovery can also be used by the Network plugins to provide an effective multi-host networking solution.
I think Docker Swarm has fixing this on the roadmap, but for now I think Kubernetes is the only thing to take into account the fact you'll probably want to have more than one node in a Docket cluster.