If they're homing missiles, you could try to have them shoot at 90 degrees to the cannon firing direction. They'll mostly arc around the cannon fire on their way to the enemy, unless the range is extreme. Alternatively, you could use beam weapons as backups. They may not quite fit your use case, though
I can kind of see where the devs are coming from with regard to realism. If I had an RPG-7 with a bore-mounted machine gun hanging off of it, I wouldn't be surprised if some machine gun round clipped the rocket on it's way to the target. However, I think I more agree with
Panpiper - 3D space is huge, and object intersections are relatively rare. A few inches is a miss for a bullet, so it doesn't take much thrusting from a rocket or missile to displace it's path from a co-linear bullet trajectory. I must say, though, I relish being able to manually shoot down incoming missiles. That wouldn't be all that possible with a more realistic system.