I usually find that larger ships handle defenses better than smaller ships.
[Warning] Wall of text.
A thought experiment I did a while back was to have 2 opposing fleets have 100 attack, 100 defense, 100 hp, and infinite weapons (so they can kill as many ships as it had damage to go around). The difference was one fleet was composed of 1 large ship, while the other fleet had its stats split equally amoung 25 small ships (4 attack, 4 defense, 4 hp each).
1. Both fleets did average damage and average defense. In such a battle, the fleet of smaller ships did no damage to the larger ship. Why is that you ask? Well the smaller fleet attacked doing average damage, which was 2 per ship was not enough to over come the average defense of the huge ship. When the first small ship attacked, it did 2 damage vs. 50 defense (reducing the max defense by 2 to 98 defense), the next ship did 2 attack against 49 defense (the average of 98 defense0, third 2 attack vs 48 defense (do you see a pattern?). When the last ship attacked, it was 2 attack against 26 defense. When the larger ship returned fire, it did 50 attack, which is more than 2 defense and 4 hp. With these numbers, it could kill 8 opposing ships. Since the fleet of smaller ships couldn't damage the larger ship with full fleet, they smaller fleet had no chance.
2. Both fleets did maximum damage and maximum defense. In such a battle, the fleet of smaller ships still did no damage to the larger ship. Each ship did 4 attack, times 25 ships, is enough to bring the defenses of the larger ship to 0, but at that point they were out of attacks to make to do any damage. However, the larger ship did 100 damage against ships of 4 defense and 4 hp. It could destroy 12 ships per turn. Again, if the fleet of smaller ships couldn't damage the big one with a full fleet, then they have no hope with reduced numbers.
3. Average attack, no defense. In the first round, both sides deal 50 damage to the opposing side. Without defenses, all damage is applied. The fleet of smaller ships kill no one, but the fleet with the big ship kills 12.5 ships. Next round, the fleet of smaller ships (with their reduced numbers) deals 26 damage and the fleet with the big ships deals another 50 damage. The remaining small ships are destroyed, and the big ship wins, but has to leave for repairs since it has less than 1/4 of its health remaining.
4. Max damage, no defense. Both sides kill each other in the first round.
5. Fleet of smaller ships gets to split 200 attack (instead of 100). All get average damage, and average defense. The fleet of smaller ships deals 100 attack (which is average) and pounds down the defenses of the larger ship to 0, but then the larger ship gets to fire back killing enemy ships. The larger ship will win without a scratch.
6. Fleet of smaller ships gets to split 200 attack (instead of 100). All get maximum damage, and maximum defense. In the first round, the fleet of smaller ships deals 200 attack. That is enough to deal 100 damage to defenses to bring it to 0, and the remaining 100 is enough to kill the larger ship. The larger ship gets to retaliate, dealing enough damage to kill 12 enemy ships (12 out of 25). The fleet of smaller ships manages to win with some loses.
7. Fleet of smaller ships gets to split 400 attack (instead of 100). All get average damage, and average defense. The results will the be same as in experiment 6. The average damage of 400 attack is the same as the maximum of 200 attack.
As you can see, the larger ship really out performs the smaller ships because it can concentrate all the firepower behind a strong defense and plenty of hit points. The fleet of smaller ships fails quickly when they lose ships and in turn lose firepower (because those guns were mounted on the ships that got destroyed).
You might be asking why I used averages. The reason is that it becomes more pronounced when you are using a lot of ships as opposed to a few ships. The impact of a high roll of 4 on the smaller ship is insignificant to large ship roll of 19. Low and high rolls might as well not happen in these experiments.
Oh hell, lets do it anyways:
8. Fleet of smaller ships rolls maximum, fleet of big ship rolls 25%. Only the last 3 smaller ships deal any damage to the larger ship. The 4th last deals 4 damage against a defense of 4 (25% of 16) which is 0 damage inflicted. The 3rd last deals 4 damage against a defense of 3, 2nd last is 4 vs 2, and last is 4 vs 1. The total damage done is 6. The larger ship gets to retaliate with 25 damage (25% of 100). It is enough to kill 3 ships. Those last 3 ships that were able to deal damage are now destroyed. The fleet of smaller ships have lost.
9. Fleet of smaller ships rolls maximum, fleet of big ship rolls 10%. Once the defenses of the larger ship is reduced to less than 40 do the smaller ships get to do damage. That means the last 9 ships get to do damage. In total, they deal 22 damage (2 deal 1 damage, 3 deal 2 damage, 2 deal 3 damage, and 2 deal 4 damage). With 10% firepower, the big ship gets to kill 1 ship per turn. The next round is 4 less damage toward the big ship (which is 18 damage), the next is 4 less, and the next is 3 less, etc. By round 10, the large ship has taken 86 damage and is no longer at risk of suffering any more damage.
So as you can see, the large ship can survive improbable odds. In the last experiment, we assumed that the larger ship rolled an attack of 10% of maximum for 10 turns (which is rare). It also rolled 10% of its defense 25 times for the first turn and a little less each turn. The enemy ships got to roll maximum damage 25 times for the first round and a little less each turn. They also got to roll maximum defense twice each turn. It takes extraordinary odds for those odds to happen, and yet the larger ship still won. It practically had both its arms tied behind its back and blind folded, yet it still won.
Mind you this was an extreme test, You won't find situations where 25 small ships are collectively equal to 1 large ship. Technically, 5 tiny hulls are relatively equal to a Huge hull (not quite, but you get the point), but the outcomes shouldn't be to much different. If all things are equal except the size and quantity of ships, you should bet your money on the bigger ship... unless the fleet of smaller ships have a combined firepower greater than twice the defense of the larger ship. At that point, the smaller fleet can actually do some damage to the larger ship.
The moral of the story is: If up against larger ships, favor guns. If up against smaller ships, favor defenses.