For server-server communication where you control both ends of the communication you can use WebSocket over HTTPS, you can use TCP over SSH tunnel or any other encrypted tunnel. You can use a PubSub service, a queue service etc. There are a lot of ways you can do it. Just make sure that the communication is encrypted either natively by the protocols you use or with VPN or tunnels that connect your servers in remote locations.
Socket.io is usually used as a replacement for WebSocket where there is no native support in the browser. It is rarely used for server to server communication. See this answer for more details:
If you want a higher level framework with focus on real-time data then see ActionHero:
For other options of sending real-time data between servers you can use some shared resource like a Redis database or some pub/sub service like Faye or Kafka, or a queue service like ZeroMQ or RabbitMQ. This is what is usually done to make things like that work across multiple instances of the server or multiple locations. You could also use a CouchDB changes feed, or a similar feature of RethinkDB to make sure that all of your instances get all the data as soon as it is posted by any one of them. See:
Everything that uses HTTP is easy to encrypt with HTTPS. Everything else can be encrypted with a tunnel or VPN.
Good tools that can add encryption for protocols that are not encrypted themselves (like e.g. the Redis protocol) are:
See also:
Note that some hosting services may give you preconfigured tunnels or internal network interfaces that pass data encrypted between your servers located in different data centers of that provider. Some providers give you tools and tutorials to that easily as well.