I've been having the same problem on a save converted from Flash. My ship stats showed 3 weapons equipped - 2 laser turrets & a missile turret - but the Battle! action in combat did nothing. Swapping to an alternate ship & then back to my main ship didn't fix it.
I eventually decided to hit up a weapon vendor, thinking maybe new weapons would fix it. Well, in the vendor UI, it said "Inventory Slots Used: 0/3". Buying new weapons - the same loadout as I had before - put be back at 3/3 slots used and allowed me to attack in combat again.
Best guess is that some part of the weapons got glitched in the transfer from Flash & they were some sort of "ghost" items, where they looked like real weapons and I could toggle them on and off in combat, but they wouldn't actually DO anything.
Hope this works for others.