I know this doesn't address small-base ships with a lot of health (though as noted, there's meta splash damage on that) but you could easily do a "Anti-Ship Missile" which does an extra damage or something to a large base ships. Flechette torpedoes is only 2 points for it's effect, something which punishes larger ships could be similar.
Or if you want to have a tank killer in general, do reverse prockets. A munition which rolls less attack dice based on the AGI of the defender. 5 ATK vs 0 AGI ships to 2 ATK vs 3 AGI ships. That's probably got more general spread.