Any missile (or whatever weapon) will always hit its target, regardless of accuracy. Misses only occur in the fact that the target doesn't take damage for being "hit". So really, the misses don't do anything other than effectively lower the damage of the weapon/weapons.
By thinking outside the box, it can be made that by example missile can miss or be intercepted... abilities can be used for replace usual weapons... let say that a ability use antimatter for create a missile in the same way that a bombardment platform is created... we can always code the missile like a ship, with speed, turn rate, etc... so missile can be killed by the target weapons or can miss if turn rate, or speed is lower that the target... for the hit, maybe something like the ram ability who have appear in a few mod... missile ram the target, deal damage and destroy itself...
The first mod who was created for sins was using a similar system... in fact, it was a mod for the beta sins, before the official release... and these mod was already with mines !!! the code of thee mod will not work anymore with actual version but the idea is always good...
Only back side in so case is that your antimatter is like your ammo... no antimatter, no shooting...