OK, I will paste the FULL art code I have for a working version of this.
Code:
; *** ART Parameters ***
SelectPortrait = SAPatriot_L
ButtonImage = SAPatriot
Draw = W3DModelDraw ModuleTag_01
OkToChangeModelColor = Yes
ProjectileBoneFeedbackEnabledSlots = PRIMARY
DefaultConditionState
Model = NBSamSite
Turret = TURRET
TurretPitch = TURRETEL
WeaponLaunchBone = PRIMARY WeaponA
WeaponFireFXBone = PRIMARY WeaponA
End
AliasConditionState = NIGHT
ConditionState = DAMAGED
Model = NBSamSite
End
AliasConditionState = DAMAGED NIGHT
ConditionState = REALLYDAMAGED RUBBLE
Model = NBSamSite
End
AliasConditionState = REALLYDAMAGED RUBBLE NIGHT
ConditionState = SNOW
Model = NBSamSite
End
AliasConditionState = SNOW NIGHT
ConditionState = DAMAGED SNOW
Model = NBSamSite
End
AliasConditionState = SNOW NIGHT DAMAGED
ConditionState = REALLYDAMAGED RUBBLE SNOW
Model = NBSamSite
End
AliasConditionState = SNOW NIGHT REALLYDAMAGED RUBBLE
That model has 6 missiles and they all hide/show properly

I suspect the problem is with your model. Two solutions:
1. Hierarchically link the Missile01 sub-object to the Fire01 bone, Missile02 to the Fire 02 bone, etc. that should work.
2. If that doesn't work, then delete all your fireXX bones, and set all the missile sub-objects to be bones. Remember to change the names of the launch and FireFX bones in the code though.
Also, if you have a model which hides/ shows the bones according to the reload state, the weapon should not have an AutoReloadWhenIdle set as this causes wierd art problems (It still works, it just doesn't look right

)