So the first time was a very convenient way to force Blair into action when he wouldn't have had a reason to otherwise, and the other two involved internal detonations? Doesn't sound like a horrible flight deck setup at all.
OK - obviously there's some conjecture that is entering into the discussion. It is, as LOAF pointed out in the 'best class' thread, tough to make definitive assessments of these ships because we *see* relatively little of them.
That disclaimer aside, I think it's pretty obvious from what we do *see* that the Connie has a compromised flight deck. I'm sorry, but it seems too easy to knock the flight deck of a dreadnought out of action. How often are the flight decks of our other carriers taken down through explosives or other means?
In addition, the deck space just looks bad. The deck gives the impression of being cramped and it appears that it is very difficult to maneuver fighters around for casual placement, let alone a scramble for launch. We don't see evidence of launch tubes - just two openings that reveal a largely exposed runway platform. I would also argue that, by the location of the hangar openings, it would be much easier for a broadside from an enemy ship to damage both with one salvo. There's not alot of protection afforded by the location of the 'runways' or their hangar entrances.
The only reason the flight deck would be designed this way is if it had to. We know the ship was built around the PTC, so it makes sense that the flight deck would be built and designed around the necessary systems that support the ship's primary weapon - and primary reason for existence. There is nothing wrong with this - if the reason for the compromise operates effectively.
As a result, I again maintain that if the PTC itself is less than 100% successful, the ship itself cannot be said to be anything but flawed. It doesn't make its reputation or achievement in battle any less meaningful (in fact, you could argue the opposite - look what they managed to achieve EVEN THOUGH...) it just means that, on paper, the ship failed to execute the intended order of battle as planned.