It´s possible to play MoO2 via Hamachi (I just did it yesterday).
We did the following:
-Installed Hamachi (I didn´t even have it) and, without changing anything in the configuration, we created a net and joined it.
-We decided who was going to be the host and noted down his Hamachi IP in a piece of paper.
-INSTEAD of opening MoO2 the regular way we clicked on the windows start button-->All programs-->Masters of Orion-->Masters of Orion 2-->Network. In the network folder you find two icons "HOST" and "CLIENT". The one who is going to host the game opens the "HOST" one, then the game starts normally and he has to choose Multiplayer-->Network-->New game. Once you do this you´ll receive a "initializing network" message: If you´ve followed this steps you won´t have problems but if you opened the game through the normal icon you´ll get a "Comm failure" message.
-Then the "initializing network" message will change to "1 person joined the game" that is the time when the other players should try to connect. They have to open the "CLIENT" icon and instead of getting to the game they´ll be stuck in a DOS-like window where they have to write: CONNECT "Games host Hamachis IP" (without the comas) and hit enter. The game will then start normally and they have to choose Multiplayer-->Network-->Join game.
-If everything is ok then you should be able to see the HOST game and join it. When the host hits start the game will load (It will take more time than in single-player) and you´ll proceed to choose or make your species BY TURNS so be patient (This is to avoid conflicts with different people choosing the same species).
I hope this helps! The game is really great and deserves a try on multiplayer. (You can even save your game and continue it later).
Let me know if this worked for you!!
(As always you should remember to check that no firewall is blocking you or hamachi and those kind of things.)