There is certainly a problem with ships and forts in the game, historically no fort was destroyed during the war by ship bombardement, instead they were taken by disembarked troops after a bombardement by siege arty (hvy mortars proved to be very effective), while OTOH the standard Columbiad 10" coastal gun was also ineffective against ironclads, the only ironclad sunk by a CSA coastal battery (USS Keokuk in april 1863) was by a Brooke rifled gun, developed during the war.
Ideally, the armoured ability, should solve the situation, the results should be.
1) Non armoured ships would be very vulnerable to coastal artillery, while armoured ships would be invulnerable (maybe another type of unit could be included for coastal rifled artillery?)
2) Forts should be very very tough to destroy by fleets. The Union player should find easier the historical method, disembark a land force with siege artillery to bombard it before launching an assault on the fort.