That is the ship I am thinking about now. I am trying squadron coordinators with antimatter lock.

I didn't play with squadrons much so I don't as well know if they are targeted by all flak-equiped ships in range or just by the ones being targeted?

I don't think there are much synergy between squadrons and regular weapons, since they are rarely focus same target, unless you are against Behemoth. So same rules apply as to usual heavy weapon slots:

1) Railgun - best short range weapon

2) Torpedoes - best cross-flotilla weapon, extra health on salvo and double DPS

3) Swarm missiles - almost as good as regular missiles here, because their rate of fire isn't halved here, unlike regular missiles, but salvo health is still doubled and damage quadrupled, paired with sheer amount of projectiles.

4) Beams - lower DPS then all above variants, but range-agnostic and thus universal module

5) Annihilator beams - install if you have them, your bombers might be left without much of the job to do

6) Blast effect battery - install only when facing swarm fleets

I can't comment on how flak works between salvo and squadrons, my quess that it is constatly applied on squadrons, one target at a time, while missile targeting works when in range on two projectiles at a time. 

Well, usually heavy weapon slots quadruples damage output, but halves rate of fire (how often module shoots), so overall DPS is about twice as big, assuming 100% accuracy. In reality it is smaller because of misses and evasion is king against heavy weapon slots. By unexplained reasons, Swarm Missiles have normal rate of fire in that slot.