If I correctly understood, you want to define in the pof of the ship a primary or seconary hardpoint, defining position, normal and maybe direction (or you can use the direction of the ship)
Then you'll have to create a model for each type of weapon, and changing the loadout will mean to change the model that will be rendered.
Also, the different weapons will come with specific properties (number/position of firing point, ammo...), properties that will be added to the ship.
If the subobject will be destroyed, the weapon will not fire anymore.
If damaged, it will not work properly anymore.
The same could be used, and I heavily suggest so, for turretts, since it'll make modder's life many times easyer
For external missles, you have to think at a realistic way to have the missle leaving the ship and start its run, either by having this exactly model to work as missle model or by having this model disappearing when the missle is launched.
When a weapon is internal, inside the hull of the ship it'll work in the traditional way, there will be no external hardpoints so no external weapon models avaiable
If you leave the hardpoint blank, nothing will happen, you'll just not have any weapon in this hardpoint
BTW, I'd also like the hardpoint system to work with other kind of stuff, like escape pods. In the SW rebel corvette I have 8 visible escape pods, and I'd like to have those pods destroyable, launchable or maybe not mounted from the beginning. Nothing that we can't do already (almost) but an hardpoint method would make it easyer.
Also, the hardpoints could come handy in some multiplayer mods, for example, there are weapons laying in a melee arena, and you can pick em up only if you have avaiable slots.
We may assign different equipment to the different hardpoints, for example extra fuel pods or additional thrusters avaiable on the secondary banks, in place of a missle rack
So, the different models (a pof each?) will have their own properties, something like
hardpoint: 1 (the type of hardpoint where it'll be mounted: 1=primary, 2=secondary, 3=turrett, 4=other)
object type: (name of weapon/equipment)
ammo (for fuel pods and similar too):
harpoint and object type will be redudnant if you use only primary or secondary banks
and in the pof they'll have their own normal, docking point, firing point, rotation axis if turretts, etc
Edit: could this cover docking points too? I mean to consider them just as hardpoints, in case you want a ship to have a visible cargo from the beginning, or something like that.