Annihilators's biggest strength is being a spammable 400 dps gun at 0 flux with very good ammo capacity. Because of the number of missiles, it tends to overload PDs and block incoming projectiles. Like all missiles, they really become scary when you mount several of them.
As far as i know, only the Enforcer (to some degrees), Dominator and Onslaught can properly spam Annihilators. The AI is a bit underwhelming with those but mounted on a flagship, i'll always take Annihilators over any torpedoes.
As Megas said, they are not the best in long fights, especially if you are playing with a solo flagship. However they felt very strong if you had a whole fleet to back you up during the battle.
For a large Annihilator... To be honest i also wanted something like this at one moment. Annihilators are very strong in numbers but very few ships can actually boat them with a large missile mount on top of that. The Astral have two large missiles but it's the last ship you want to send brawling the enemy. The Conquest also have two but forward facing, by using those you'll lose quite a bit of your broadside firepower.
The only vanilla ship that could become really scary would be the Aurora, 1 large Annihilator + 4 small ones. With the two medium energy for shieldbreaking, the Aurora could become really mean.
But other than that, a large Annihilator doesn't feel that threatening, mostly because there's no ship that can get the most of it.
A large Swarmer however, now this could be fun.