It’s worth noting that even with high health parts, and part collisions set to none, missiles will still destroy you, by breaking connections. As far as I know, there is no way to avoid this at all, its just how sp works.
It’s best just to avoid getting hit at all by using flares and chaff or whatever.

There's only a few ways from what I know, and they're not always surefire:
-Set your part mass really high. The parts usually survive, but will still break apart.
-Use high-health parts. Same issue as the first method, but at least this one can improve survivability to guns while not hurting flight performance.
-Set partCollisionResponse to None on all parts. Tedious, but it can help the aircraft be more durable, and if properly executed can even make the plane immune to crashing, but missiles can still threaten it. I should also mention that explosive weapons (except cannons) may not work properly if you use this method on them.
-Damage models. As you may know, a part, when destroyed, will often destroy the parts around it. But if a part attached to a detacher or rotator is destroyed, this won't happen. Use rotators and/or detachers to build a damage model (similar to what I did on my M-War II aircraft like the LF-4 or Mu-19) and you MIGHT stand a chance. I will warn you though, this method probably has the least success of the ones I've mentioned, at least regarding how to survive missiles. Damage models are really ideal for gun combat.
-The most successful method from my experience, is not the victim, but the threat: setting the explosionScale variable on missiles to something below 0.75 can make missiles survivable, only issue with this tactic is that they might end up not doing enough damage, especially to high-durability aircraft. If properly executed, though, you can make somewhat survivable missiles.
-I'm cheating with this one, but the best way to survive a missile is not to get hit by one in the first place! Flares, chaff, hiding behind terrain, staying too close for the missile to maneuver to you, whatever floats your boat.