I've read your post again and it suddenly became very vague. If you set the weapon to use ammos only at the end of burst cycle, it means it will use only one ammo per burst, no matter how big the burst is. If you don't, then a rocket is used for every rocket fired. Now, your turret is two pods. That means it is two outfits, right? If it is not then how do you expect nova to understand that?
If I'm right about how you want them to work, you should make 2 outfits for the turret. One weapon. Now have both outfits grant the same weapon. One of the outfits is massless, invisible and can't be sold or seen or anything. The other one grants the invisible one when you buy it and removes it when sold. What this will do is simple. It will act as if you had two weapons for nova, but the user will only see the one he bought.
I'm not sure, though, if nova will like that, as associating two outfits to the same weapons means that if a ship is equipped with it by default, it cannot tell which outfit should be granted. A possible fix would be to set it in the outfits, but then the AI doesn't use outfits and will not be able to use them. If no ship has more than two, then a cron could check if you have one of the invisible ones and none of the "real" ones, remove the extra and grant a real one. Should work. If no ship has more than two. And if nova doesn't fry its own brain with multiple outfits of the same weapon.