I only disagree about the need to do anything about big ships fighting small ships.
I have the same questions about accuracy, agility, and speed, but there are definitely reasons to build different sized ships.
First, it takes a long time to reach the largest hull sizes. You'll only have the smaller hulls for the first half or more of the game. And remember, if you have a lot of high production shipbuilding worlds that can turn out a large hull every turn, you've probably already won (against the AI.)
But what if you're not there yet? You might have a lot of low production worlds that can turn out just as many hit points worth of small ships every turn.
Another reason to build different sized hulls is to set the type of ship you produce. You could have a large support ship armed with missiles and as small assault ships to your logistics level armed with short range mass drivers. This fleet can push deeper into enemy territory. You send a stream of smaller ships to the fleet as you go. Yes, as you point out, the small ships are destroyed, but they soak up damage for the larger ship. And as you're able to produce them faster, a stream of the small ships can keep the fleet at the logistics limit, turn after turn.