Just wondering if the attack bonus from a flagship would apply to the dice count of a secondary weapon, like Dorsal Weapons Array.
No the flagship doesn't give an attack bonus it gives an increase of the ships primary weapon stat line.
Also for that matter do attack die bonuses in general (range bonus not included obviously) apply to secondary weapons?
Secondary Weapons can be increased by abilities that add + X attack dice
So for example I have two ships with Dorsal Weapons Array, one is a flagship that gains plus one attack die and grants plus 1 attack die to a friendly ship in range 1. Can both ships fire their Dorsal Arrays with 4 dice?
In this example the flagship would roll 3 attack dice, and the friendly ship if in range 1 of the flagship would roll 4 attack dice.