From the future blurays extras
Q. Why wasn't the fleet able to shoot her when they saw her coming directly at them?
A. The mechanisms for the ballistas were not properly treated for operation at sea and rusted overnight causing difficulties aiming.
Honestly though, this is probably the only thing [from complaints of this episode] I feel is defensible from a strategic point of view. Last time there was literally zero attack plan with the dragons. She turned the corner around the mountain, and there a flotilla suddenly appears. OK, dragons, this'll be easy. Oh, wait, they have a massive number of scorpions (type of ballista). Well, they're committed to the dive/charge toward the boats. All from the front, where all the scorpions are already conveniently aimed from the front of the ships.
Never you mind that any ballista has never been a solid example of good anti-air defense, for they were never developed with that in mind. You should note that they even made these scorpions modified to have greater elevation control, apparently nearly straight up -- clever, but that doesn't solve the rest of the weaknesses of the weapon type against close air support style flying attack beasts.
See my prior post regarding scorpions for more. But in general, this time Dany knew the tactics of the enemy, knew their capabilities. This time she used her dragons like attack aircraft, first coming in via a surprise assault from directly above.
Remember, this isn't modern warfare - they don't have speedy ship to ship communications, something critical when dealing with a high speed vertical assault. Nobody was apparently looking straight up, which makes sense because Dany hasn't used that surprise assault tactic before that I recall, the dragons have always made an entrance - because they're fucking dragons, what are you gonna do? They adapted, then she adapted. Nobody involved here is familiar with flying attack weapons other than trebuchets.
So Euron spots her up above, but can he readily communicate that to his whole fleet? Doesn't appear to be, as only a few ships, presumably those closest to his flagship, get shots off. After she dives down and starts the strafe runs, the entire fleet is already doomed. There is no way they can adjust aim fast enough to keep up with her, and that remains true when she starts hitting the turret towers. As hard as it may be to imagine a 747-sized fire-breathing beast just zooming around getting the surprise on all those turrets, they aren't all in visual contact with each other (from across the way that is) and they fly too fast for most of the scorpions to ever get even their aim lined up correctly.
The more and more I think about those details, the more I come to see that they presented all of that appropriately. It was a matter of adjusting to the tactics. Cersie's army would have had far greater success if they had saved the element of surprise to when both dragons approached the city. Dany wouldn't have adjusted tactics, she had never seen so many scorpions deployed before. Obviously they hoped to take both down before the battle but given the possibility of at least one escaping, their own defensive tactics could stand to fail. Fail they did.
Obviously the show could have made it look far more protracted, but that's where the showrunners let us down this season. They may have had GRRM's main story objectives, but they wouldn't have had the exposition that comes with the POV character chapters. Dany's destination has been telegraphed because it is difficult enough to translate exposition to visual story, more so when that exposition doesn't even exist. We don't get to know what she was thinking and mulling over, and due to the rushed script, we don't even get a hint of that inner turmoil.
And oddly enough, this got me thinking about something in terms of narrative: GRRM's often been cited as a notorious example of a writer who is willing to "kill his darlings" because so many main characters that obviously seemed to be protagonists wound up perishing. I'm coming around to thinking that, no, GRRM may not be the maverick of darling killing. From the name of the novel series (A Song of Ice and Fire) to the telegraphed story arches for both Dany and Jon, I think those were his ultimate darlings. I don't know if it was in the novels (I would expect it to be) but Jon getting a reprieve from death certainly seems to, in hindsight, give weight to that idea.