It's supposed to be huge. Active camouflage and such make it a much less noticeable target, and it's multidirectional turbines make it suprisingly nimble. Hence why unguided missiles would need to be fired from pretty nearby. Fragmentation missiles would only be effective if there's no internal armor. Which there is. It's needed to keep the compartiments intact, protect and anchor the installations that ensure active camouflage, and provide enough structural integrity for when a 20 ton dragon slams into one of the balloons.
There are no blind spots.* That model I posted was inaccurate, but the closest thing I had. The whole thing is an integrated structure, so the runway and the two balloons are fact conneced at multiple points. When you manage to break through all that, which is quite an achievement, the ship is lost anyway as most of it's critical system have been destroyed. As for loosing one of the 2 balloons, it's highly unlikely that all compartiments will be breached, even then, the helium takes some time to fly away. And even then, gyros can ensure a bit of stability, allowing the ship a safish landing.
The ship is not indestructible. However, there's no 1Hit KO scenario possible. Damage is grave however, as the ship is fairly hard to repair. Defense systems are nice, but overwhelm able. The ship lacks in offensive capability, and while it's stealth system is very good, it's not perfect.
*At least, there shouldn't be.
Don't forget square/cube law when scaling up things. Works for Cheetah's too.