I've often wondered about coastal fortresses myself. I haven't built one in years. I believe that last time I built one, it was destroyed when an enemy ship went near it, someone launched a shot, and that was it: fortress was gone. Since then I figured it wasn't worth building them, whether it was a bug or not.
Now I know. And knowing is half the battle.
I tend to keep alot of artillery in my coastal cities, then when I get bombers I keep a few fighters (for 'radar') and bombers in cities that are getting bothered by enemy naval bombardments. The attrition is excellent. I tend to only use navies to protect allies or move troops for an initial intercontinental assault.