I don't have the rules in front of me and I might have read your post wrong, so sorry ahead of time if I am pointing out the obvious.
Bomb Dice= total number of bombs per game.
Ship may bomb a 2cm square directly below the ship.
May bomb once at any point during the movement turn.
Roll1D6 per bomb dice used up to a maximum of 3 dice.
Each additional bomb dice used above 3 adds a +1 modifier to each of the three bomb dice rolled.
Damage to area = 1 point per 6 rolled.
Cannot bomb airborne vessels.
Any vessel inside the 2cm target square takes 2D6 hull damage per point of area damage.
Bombs (alternative rules):
At the start of the game physical features are identified as targets for bombs.
Each target is assigned structure points. Civilian buildings are 1-3 points. Fortifications are more.
Hits are records as per normal bombing rules.
At the end of the game a D6 is rolled for each target.
Add this roll to the number of hits on the target.
If final score is equal to or greater than the target’s structure points the target is destroyed.
So if you want three bomb dice with a +3 bonus you would have to drop a total of six bombs from the ship.