If all missiles could be intercepted then saturation attacks might be the solution to getting through a cap ship's defenses, combined with decoys, radar jamming etc. Pretty much what happens in the real world today.
You would have to mount beams on all turrets.
You say that like its a bad thing
Theoretically you could create a fast firing low power AAA beam for this. Too weak to be of much threat to fighters and bombers, but great at taking out missiles and bombs. Or, you could create a CWIS type turret to achieve the same. Very high RoF, very high projectile velocity, but low damage per shot.
Also anti-missiles. I have had some success using harpoons in single fire mode to shoot down bombs. You could imagine a fast-targeting, fast moving and multi-locking swarm missile would be useful for taking out multiple warheads. These could be mounted both on interceptors and the cap ships themselves. Again, nerf their power against fighters and bombers for balance reasons.
It would be cool if the CWIS, flack and anti-missiles were ammo-limited, and the 'anti-missileAAA' beams RoF has to be scaled back after heavy use due to energy draw and thermal build up. At the start of an engagement the amAAA, CWIS, Flack and anti-missile screen would be almost impenetrable, but as the munitions start to run out the cap ship becomes more vulnerable until it has only the AAA beams are left. These too then start to become less effective as their RoF has to be lowered.
This would make Shivan style multiple bomber waves a viable tactic. The first waves would be expended to use up the defenders munitions, the later waves would then go in for the kill. This would make for an interesting escort mission.
Waves 1-3: Ha that was easy, my cap ship has 'nary a scratch!
Waves 4-6: Ok, this is getting a bit tricky, my cap ship is getting a little beat up
Waves 7-8: Oh crap, my cap ship is getting wrecked
Wave 9: Noooooo, my cap ship got blown up