I'm not sure if I'm missing anything but I can't see a way to attack a city that takes up all the land on an island without using missiles or planes - land units can't disembark and can't attack the city from water, and ships don't seem to be able to pillage or attack either. 

Also is there a way to rebase missiles or do they just stay at the original silo? 

There should be amphibious units in the game that would allow attack from embarkation to land (should be).

I haven't figured out a way to take them out either.

Wait this is a issue? What? This sounds terrible.

Had the same issue. Carpet bombed or nuked it. Satisfying, but probably should  be able to also siege/conquer island cities.

SpicyCrab wrote:

Fan wiki says that only Howitzer and Helicopter Gunship can attack fortifications. Kinda weird that ships with cannons can't do that.

Yeah the Howitzer and Gunship are the later era versions of siege engines, although I think it would be some better UX if it didn't just say 'research some siege weapons' after they become irrelevant. Ships should also be able to attack fortifications though, but been able to start attacks on land targets from the sea at all would be nice.

I think all units should be able to do disembarking attack on city tile, but with strong debuffs depending on the fortification level