How can I deploy and execute an application on a device connected to a remote system?

From the adb tag wiki:

Android Debug Bridge (adb) is a versatile command line tool that lets you communicate with an emulator instance or connected Android-powered device. It is a client-server program that includes three components:

1. A client, which runs on your development machine. You can invoke a client from a shell by issuing an adb command. Other Android tools such as the ADT plugin and DDMS also create adb clients.
2. A server, which runs as a background process on your development machine. The server manages communication between the client and the adb daemon running on an emulator or device.
3. A daemon, which runs as a background process on each emulator or device instance.

adb connect command is used to connect the local adb server with the adbd daemon on a network connected device. But what you want is to connect the local adb client to the remote (running on another system) adb server. The default behavior of the adb executable is to connect to the local instance of the adb server. If none found it would try to start one. This approach works great for most environments where all development is being done on a single system. But in more complicated environments it may result in multiple instances of adb server being launched. And because adbd daemon only supports being connected to a single adb server at a time - the device will get recognized by one system and will appear missing everywhere else.

So in order for adb to reliably recognize devices in those more complicated configurations you need to tell adb to stop guessing and manually specify which part of adb (i.e. server or client) should be running on which system.

First off make sure that you have the same and sufficiently recent version of adb (the latest Google official version usually works the best) installed on both local and remote systems. And that no adb servers are currently running on either system.

Then start an instance of the adb server on the remote system (the one which you will be plugging the devices into) with this command:

adb -a -P <PORT_NUMBER> nodaemon server

Now you can force adb client on the local system to use the other (remote) server instead of starting its own (local) instance by adding -H <REMOTE_IP> -P <PORT_NUMBER> to your adb commands:

adb -H <REMOTE_IP> -P <PORT_NUMBER> devices

Alternatively, setting ANDROID_ADB_SERVER_ADDRESS=<REMOTE_IP> and ANDROID_ADB_SERVER_PORT=<PORT_NUMBER> environment variables on the client side would allow you to avoid having to specify the <REMOTE_IP> and <PORT_NUMBER> for every adb command.

And if omitted the <PORT_NUMBER> would default to 5037.

This official built-in solution for adb orchestration is not a mutually exclusive alternative to the SSH tunneling - it just addresses another more important issue. You can add tunneling on top of this to add extra security or help with routing issues in a multi site network environment. But the tunneling alone will not be able to solve all the adb connectivity problems.

Same goes for the virtualized environments - running multiple adb server instances between host and guest systems will also result in the adb connectivity issues.

Perhaps this will help:

Its a java library that I've developed few months ago specifically with that remote adb commands in mind. The basic idea was to provide some abstraction layer where devices could be similarly accessed on remote machine as it was locally connected. Check it out:

https://github.com/lesavsoftware/rem-adb-exec

PS. and it uses SSH tunnel so it should be secure enough.

What about using SSH to connect to the machine on which your device is attached and issue ADB command from there ? This is at least what we do in our company where we have dozens of devices we control like that.