I have a vague recollection of this issue (meaning, bonuses not showing up for one player) popping up at least once in some other game.
Anyway, I could send you the turn with the same composition, but you'll have to give me a screenie of how it looked like, since I don't remember exactly.
However, by my reckoning this is roughly how it should play out - remember that my fighters and bombers have 40 armour, or 44 if they're elite, due to the battlemaster bonus. This pushes the damage table to 2:1 or 1:1 respectively - which gives 10% or 0% chance of instakill even by a dreadnought. Furthermore, even at 12 accuracy, unspotted fighters have 11 agility, so roughly half of ranged attacks miss, and most hits don't kill.
On the other hand, a 30 damage fighter with the relic gets to roll in the 1:2 table - which is approx. half the damage it receives from a dreadnought hit. (no, that's not right, you also have the battlemaster, which gives 1:3)
Additionally, lots of dreadnoughts means very few close combat attacks (which are most numerous at 4 a pop), whereas I had lots.
What mystified me, though, is how my high-rank ships were being targeted when they shouldn't (especially in the round I was just moping the remains and my hauler got hit). This goes against my understanding of the mechanics, unless there's some hidden assassin-like targeting scheme for regular ships.
But eh, fuck. I know it's a major setback, which is never fun, and I also get the feeling the game mechanics are at the very least absurdly biased towards the attacker. This might be a good moment to pause for some discussion of these issues.