Hi NT_Jedi,
To answer some of your questions:
The AI usually sends the assassins to your capital.
It should know to load them into boats to reach your civ if it is on an island because it uses the same logic as ths spy.
As far as spamming solutions...
I recommend playing with my training barracks (which I suggest in the readm file). It makes it so barracks give 0 exp to a unit when it is built and give it more experience over time. That will give the edge to the defending assassin who stays in the city to defend instead of going out and doing missions. Even without that though, the defending assassin's civ will eventually get the upper hand because a defending assassin has 0% chance of dying while the attacking assassin has a substantial chance if there is a defending assassin. Also, in a game with mroe than 2 players you will leave yourself vulnerable to a third player if you send all of your assassins on missions.
Roger Bacon