I see where you are going with this, but it would only eliminate the need for some weapons... Think about it, the harpoon and sabot are completely different missiles. Changing the warhead on them would unbalance the way they work too much IMHO.
Maybe what we should see is instead have weapons that are repeated in each mount class, just be one weapon that scales depending on what mount it is in.
For instance, we have a small and medium mount for harpoon. They are identical except that the medium size shoots two missiles and has nine more rounds. I imagine if we get a large harpoon mount it'll shoot three and have maybe thirty rounds. Otherwise they are the same weapon...
So it would work like this: I buy a harpoon launcher, I then put it in the slot I want, it changes it's picture and stats to reflex that. The stats could be either hard coded, or just have a base one that increases depending on the mount type. Also, there would be a flag that says what mounts it can fit it.
This could cut weapons down by at least 30%, while still having them.