Table 1: chance a missile (-4 target) survives a round of fire, based on hit bonus (crew quality, target computer and weapon accuracy) and number of turrets per incoming missile.
The upshot is any reasonably modern warship with a significant laser: incoming missile ratio will shoot down the bulk of the missiles in the fire phase. However all ships in the same hex as a detonating missile get another round of defensive fire if the missile commits to detonate. The ratios will change because in this salvo all the dead missiles are discounted.
Say your a single cruiser with a total of +5 targeting and can defend against 4 incoming missiles with 8 turrets. In the initial "normal" shots on average 25% of incoming missiles survive, leaving a single missile. This now faces a second round of fire at the 8:1 ratio, with a 0.39% chance of survival. To all intents and purposes the ship is immune to missile attack at this level.
The upshot is that in major fleet actions with significant warships missiles are almost useless. They of course force ships into close defensive formations to maximise defensive firepower, but not much more.
Now in minor actions with less gunned targets missiles do become useful. If your target is an Aconit and you shoot a pair of missiles she only has a single turret to defend against both (typically at +4), and so after the first shot there is a 40% chance both missiles are still inbound, and defensive fire in the detonation phase still has a 40% chance. There is a good chance of a missile getting through, a good chance if it does it will get hit, and a good chance if it does of wrecking the Aconit.
In a major action it's likely that you'd want to stack up and try and provoke the enemy to spend missiles attacking you whilst you put up a wall of flack. You might send out fighters to shoot down missiles etc., and try and husband yours. This is because if the missile is fired whilst the enemy is engaged in close combat then they have to choose between devoting their main fire to enemy ships or to missiles. The best use of missiles is probably to be threatening enough to force the enemy to devote their fire to them, and thus gain an advantage in the gunfight.
The best use of missile frigates like the Kennedy would thus be behind the main battlegroup, darting around, dodging missiles and throwing theirs into the fight. However, without a battlegroup fixing the enemy in a gun action the chances of inflicting damage are minimal.
