Just to point out Cam, those weapons are not anti-small ships, they are small ship detterents. Now if they aren't deterring folks form shooting up your ships, then yes, they aren't doing their job. But they aren't meant for wiping out bombers and fighters. Unfortunately for you these ships are balanced for team work now, as they always should have been. They aren't solo pwnships of doom as they were in 4.82 nor are they pointless bauables as they were in 4.84. The balance may not be quite right yet, but it's getting better. Your capital class vessel is now better at shooting up other capital class vesels.
I'm going to use a Warhammer 40k reference here as it can be used as a metaphor.
I have an Imperial Guard army which is monstrously good at shooting, ignoring the troops of course as they are useless in all situations, if I want to take out a Tyranid army, which is awesome at close combat, I need to do one of two things, either gear up my special units with close combat weaponry and take close support heavy options, or I need to maximise my ordnance to do as much damage as is inhumanely possible before they arrive to mince me. Either way I lose some functionality and if it all goes tits up I die. And trust me it doesn't take much for it all to go tits up with a Guard army.
Capships are like this now, if you want to counter bombers and fighters you have to specialise a lot, but that makes your ship relatively useless against larger caps. If you want to rip apart the big stuff you lose the ability to shred small ships. One or the other but not both. Now if the option to specialise in blowing up smaller craft isn't there, then you have a problem. But if you're intentionally losing it to be able to make bigger ships cry then nothing is worng.
Saint Del is considered a holy healer of diseases of children, but also as a protector of cattle.