With my hundreds of hours in game, you'd think I'd know this by now, but I haven't really tried it yet. Anyways, when launching port strikes via bombers, does one target the sea zone or the state the port is in? 
I believe this is correct. I don't think you actually see where the enemy fleet is docked (this might change in a future Intel/Espionage expansion)I believe you can only see details on a fleet if it is yours or belongs to one of your allies. In spite of that, a port strike mission always knows if targets are available, and if so, it knows exactly where to find them.