Hi! While I haven't worked with the Master Server Kit I just happen to have been playing with Unity networking, running a server for a game I'm building as a hobby. I think I can help clarify things for you:

Open port in digital ocean Ubuntu 16.04.

By default your ports will be open. When you are ready to set up a firewall this guide will walk you through the process.

Where to put my ZoneServer.exe,RoomServer.exe,and WorldServer.exe in filesystem?

You can place them anywhere. Personally I have two server systems for my game and store them in folders under /opt like /opt/gameserver1 and /opt/gameserver2 but that's just my preference.

One thing to note is that you'll need to build the server for Linux. On the build settings screen select Linux 64 bit and check the box for headless mode. This allows your server to start up from the command line without the need for a graphical environment.

How can i access suppose ip:port/Zoneserver.exe

You won't have to direct your connection to the name of the executable. When you start your server it will bind to the port specified and all connections to that port would then go to your Zoneserver. Here is the connection string I am using in my project...

using UnityEngine;
using UnityEngine.Networking;

public class main_loader : MonoBehaviour {
   NetworkClient myClient;

   void Start() {
      if (SystemInfo.graphicsDeviceID == 0){
        if(true){
            isServer = true;
            startServer();
        }
        else {
            isServer = false;
            startClient();
        }
   }

   void startClient () {
      myClient = new NetworkClient();
      myClient.RegisterHandler(MsgType.Connect, OnConnected);
      myClient.Connect("server.example.org", 4242);
   }

   void startServer() {
      NetworkServer.Listen(4242);
   }

}

The Start() section will determine if the code is running as a client or a server by checking if there is a graphics device. Since only the server is built to run headless this is a reliable method. Then if the code determines it's a server it will run startServer() which begins listening on port 4242. If it detects that it's a client it will try and connect to the server at "server.example.org" on port 4242.