I suppose you could fake a flame at the back of a missile with a deformed cone and some alpha and some emmitter material tricks or even a halo or two, then you could just use particles to dupli’ the missiles from a plane emmitter, subdivided so that each vertex corresponds to a pod.
 - You can make the flames from a statit particle emmitter, as you can place a satic emmitter inside a dynamic emmitter ( :o ) but for the number of missiles you’re referring to… DONT!
Then you could play around with the various forces and guides to get the missiles to appear to track individually.
Hmm - trick would only work if each missile travels the same distance. i.e. each particle has the same lifetime.
(Hey, 2.40’s new “Unborn” particles feature would show the unlaunched missiles! - bit of a pain on polys though!)