Missiles have an issue with guidance and the target lock system. Not to mention not being piloted by something intelligent, whether artificial or not, does mean ECM might have a bigger affect on it compared to fighters, as it's more likely the fighters have their components shielded from such.
I think remotely-guided missiles coupled with instant quantum communications can give one the benefit of having intelligent pilots without actually needing all supportive stuff for pilots. And if you can shield the fighters from whatever by whatever, you can shield the missiles the same way.
I guess the realistic issue with bombers is if we can carry the bombs that far in, why not just launch the bombs instead of the bombers? If a bomber doesn't get shot up, then a missile won't either.
Indeed, which is why the way the FTL works in my system is integral to the justification of bombers.
Very short version: the FTL drive ('blink engine' or something), once activated, propels a ship forward at speeds several times of c. While doing so, it has no physical presence in the way we know it (could expand on it, but won't, would take too much time). However, it keeps going until it either runs out of fuel or it gets pulled out of the jump. This is because everything that has mass sends out a 'gravity field', the more mass the bigger the field. And the chance (and distance from the object) of an object forcing you out of jump increases with both your and his mass. The distance at which a ship is forced out of jump isn't always the same though, but follows a probabilistic approach, like a bell curve.
So two fighters jumping at each other could get into 20 meters from each other, while two 500 ton capships jumping will be forced out of jump at 200 kilometers (random numbers for sake of example). Moving to other starsystems is done by 'aiming' for that star and letting the engine go, meaning you will stop somewhere near the star, but this could be 10000 kilometers or 13000 kilometers away (random numbers, would need to determine a base set of numbers to make it work). Jumping again after being forced out could be handy if you drop out sooner than wanted, but once you get close enough will only move you a few meters (but, due to the nature of the system, you could jump and land 10 cm away from that sun, but the chance would be reaaaaly smal).
So now, two fleets engage. Capships drop out at certain distance. One launches big missiles with blink engines. But, if the other ship now sends out a 'net' of drones to force the missile out early, they may only lose one drone (where you just lost an expensive blink engine).
Fighters, however, can close the distance enough to shoot their weapons since, because of lower 'self-mass'/'self-gravity-field' they are forced out of jump much closer. So now the fighters need to clear a path through the drones to either let a 'blink-missile' get through without dropping out of jump to soon, or have bombers do it themselves.
There is more to it, of course, but that's the gist of it.