i get around that problem by only using the show models features on ships with external hard points or bays which use a standard missile size, and use it for things like gatling barrels. pirate ships which carry bombs do so externally or in large open bays (which are used to launch combat drones, a feature which is currently somewhat experimental right now). ultra fine rocket racks i usually just use for small things like tempests and other rockets, and they need not show ordinance. larger single shot anti fighter class missiles i may have shown, would look sorta cool on the new vulture im (slowly) working on. since the weapons are only revealed when you arm the bank and the missile doors open. all those custom ships and missiles can really bring out the awesomeness of the engine. thats why i started working on the pirate "species" so i could use more features without restrictions being imposed by existing freespace models. its worked quite well.
all it really requires is new, smaller models. missiles are only large so as to be somewhat visible. you can do like other games where the thruster flames are so intense the blot out the missile model all together. its just a matter of making the missile look good, while being

smaller that were used to. even then many freespace models (even htl versions) are not suited to the visible weapons system. disproportionate missile tubes between models is a big problem, so i adopted a few standards for the sizes of missiles, gatling guns, ect, so that they would be more consistent with my ships.