Will the Ballista be able to intercept other missiles, such as S9 torpedoes from a bomber or the Hercules' A2 bombs?

This is functionality that we want all ships to have in the future, not just the Ballista. Being able to target incoming ordnance items is critical to keeping larger ships and ground outposts intact. Of course, targeting is just part of the equation; it certainly helps to pick a suitable weapon system for the intercept.