Fighters are ships and follow the ship rules. Missiles are single shot weapons with a single use drive and a lot of restrictions on their use because they have zero, or minimal, on-board intelligence. They don't have anything like the huge flexibility of ships, so they make a much more predictable target.
I know beam fighters are powerful - I have been saying that for years

The recent missile changes were a way to make missiles more competitive vs energy-armed ships (including fighters), although a lot of players still think missiles are OP as well, so its probably more balanced now.
The reason beam fighters are doing well against NPRs, is that as a result of the missile changes I reduced the fire control numbers for NPR ships to allow more room for weapons, without considering the impact on fighters. I need to review automated designs for the next version and give the escort classes more fire controls. Players can make their own decisions on the optimal number of fire control, but that is less of an issue except in multi-race starts, vs the swarm or when the NPRs get fighters.
EDIT: I've made the changes to NPR fire controls, so they will be more effective for the next version (and for any new NPR designs in my current campaign).