Except provide a ridiculous amount of extra armor for the larger ships. They get low agility, so they're easy to hit, but not to penetrate. You could potentially spend quite a while pouring fire into a Flagship and have it come out only minimally damaged. Plus, the larger ships have more attachments, so they're harder to kill anyway.
For instance: You have a ship with a small rocket attachment, firing on another person's Dreadnaught-class ship. The Dreadnaught has Heavy Armor, and Shielding. The Dreadnaught gets to add three things into it's armor roll: the Shields (+1d6), the Heavy Armor (+2d8) And it's Structure level (+4d10). So, unless they roll badly, those rockets aren't going to actually hurt jack squat.
Whereas without the Structure rules, that Dreadnaught loses 4d10 off of that roll, and is therefore WAY easier to hurt.