Second even after a missile is no longer tracking the ship will still act like it's tracking them and raise shield even if it's floating harmlessly.
Ah, but it's not floating harmlessly. That's the thing. The missile has simply run out of fuel. Until the point that it fades out of existence, that missile can still smack a ship and do damage. Another thing to note is that these "dead" missiles no longer differentiate between friend or foe and explode on the first thing they hit. A Reaper will still rip you a new one, Sabots will still fire their charge, Hurricanes will still split into a MIRV. Things like Annihilators have a range much higher than the one listed as they spend several seconds in this inert out-of-fuel state before fading. The Neutrino Corp's Piledriver-class with it's Unstable Photon Cannon is practically built upon this idea. The single missile it fires will split in flight into about 30 missiles that is an absolute nightmare for non-flak style PD. But those 30 missiles become inert maybe half a second after they split, so -anything- in the way that might normally be fine if it was a wave of Pilums will likely take some serious damage from the Photon Cannon.
I know it's not 'floating harmlessly' but it has become little more than a glorified projectile. If it's not even possible for it to hit the ship it will still raise shields towards it simply because it's near by. If a MIRV is capable of splitting it's probably because it's still flying towards the ship. Otherwise it wouldn't because it'd be flying further away and not facing the right direction. I'm not saying for the AI to ignore them but to
treat them as a projectile. I really like it when someone actually reads past the first paragraph before posting. Otherwise people leap on the first thing they see without understanding the context in which it is said.
Also, again, we cannot balance around mods. Second, even in that case because the missile is still on a collision course with the ship it'd still have it's shields raised.