Space Battle idea

The way I underrstand the game;

Missiles and Kinetics are both considered Projectile Weapons, and do Impact damage.

Beams and Lasers are both Energy Weapons, doing Energy Damage.

Armor creates Defense against Projectile Weapons.

Shields create Defense against Energy Weaponos.

Now... with that said, both weapons' class have balanced defense comparable to each other. However, on every Kinetic gun I've seen, it says they are integrated later into Anti Squad and Missile defense guns. Later in game, through research, about the time you discover Squad Fighters/Bombers, you also discover (depending how you lean on the Tech Tree), Anti Squad cannons, designed to destroy enemy squad craft too close to your ships before they do too much damage. I believe those Anti Squad guns ALSO do damage to incoming missiles, and tie into the Kinetic Projectile weapons, as it says on those weapons when mounting, they are used in sync with the Anti Squad guns to stop squads and missiles. 

SO... you already have your anti missile weapon... just might not effectively see it, but it just alters the statistical numbers if anything.