Well, if multiple scatter dice are the problem, why don't keep the rules simple:
-D6 damage if "hole" touched, 1 damage if touched by template
-range: 30-150cm, scatters 1D6, regardless of range, a "hit" still scatters, but distance is halved, rounded up (1-2=1cm, 2-4=2cm, 5-6=3cm)
- to use a nova cannon a succesful "reload ordnance"- roll is needed
- Battleship mounted NC's throw 2D6 for scatter distance and take the lowest AND throw 2D6 for damage and take the highest
Average damage is 1,78 for small Bases and 2,44 for large Bases.
This is a simple rule, without "harming" the NC: you get a drawback at small Bases at short distance, but a reasonable increase over long/medium distances. This amount of damage seems fair to me, as a NC usually costs ~20p more than torpedos and therefore should deliver more damage than a torpedo tube. the "reload ordnance" is a little "price to pay" for Dominators or upgraded Lunars without harming the (IMO already overpriced) Mars. the last paragraph is in to help the underperforming Apocalypse. It doesn't solve the problem of "Nova spamming", but this is something the players must solve by reason and good manners: at all it isn't worse than Devastor-Spam, Explorer-Spam or Eldar just using destroyers....