Well, effects are sort of take-it-or-leave-it. The only 2 effects that have one missile are the Vasari Assailant's phase missiles, and the Ogrov's torpedo.
How exactly do you want the nuclear missile firing to go? Meaning, does the ship *only* launch them or is it an ability added on to the basic Javelis? In the first case, Cluster Warheads is the way to go and you just need to change the ship's weapon effect. But it sounds like that's what you don't want.. In the second case, abilities can use particle travel effects.
For example, from the Kol's AbilityGaussBlast:
weaponEffectsDef
 weaponType "Projectile"
 burstCount 1
 burstDelay 0.000000
 muzzleEffectName "CapitalAbility_GaussBlastLaunch"
 muzzleSoundMinRespawnTime 0.100000
 muzzleSounds
  soundCount 1
  sound "WEAPON_GENERICFIRE"
 hitEffectName "CapitalAbility_GaussBlastHit"
 hitHullEffectSounds
  soundCount 1
  sound ""
 hitShieldsEffectSounds
  soundCount 1
  sound ""
 projectileTravelEffectName "CapitalAbility_GaussBlastTravel"
(notice the hasWeaponEffects TRUE a little bit above that).
In theory, you should be able to use the weapon effect from the Ogrov, for example, in the ability file and then have your buffs do the dirty.