E. g. If a fighter with one missile fire control launches missiles of sizes 1,2,3,4 and 5 at a ship that has a single beam fire control on final fire point defense with 5 turreted beam weapons linked with 100% hit chance will it only shoot down 1 of the 5 inbound missiles? In contrast, if the fighter launched 5 missiles of size 3 they all would be in the same salvo and so all would be shot down.
I do not believe that is how it works. The missiles are grouped together because they are all travelling the same speed; I bet if you were to fire different size missiles at the exact same speed they would still be grouped together. Think of it like a task group, even though you have multiple ships they are all still listed on that one task group and only one of the ships can be targeted by a fire control at once. The same goes for missiles and if anything firing like you suggested would reduce the chance to hit. With the missiles more spread out the enemy has a bigger time frame to shoot them down. A better strategy would be to shoot a bunch of small missiles with low agility and strength with larger missiles more likely to hit so the enemy's defense is taken up by the useless missiles, like decoys.
