I may be way off here, as I have never done a mode. But flashing lights, is that not part of the model itself? And the hardpoints, I know in some games is is part of the model, but if we just have relative positions to the models center will that not work? plasma leaks and these types of effects I think can be effects, similar to explosions etc. A particle effect.
My thoughts and I can be way off: A ship, with a specified hot point, fires a torpedo. Based on the hot point location the torpedo leaves from that location and heads toward the target. Once te torpedo hits, there is an explosion, this explosion uses a particle effect. And the torpedo is a 3D model, not a sprite.
The problem with a sprite is you have to create the bitmaps for the sprite to loop through and they all look the same. With a particle effect there can be randomness, not all the same.