This sounds like a personal lack of knowledge of weapon design as opposed to missiles actually being underpowered.
A problem that has been the case since I bought the game a couple of years back, that persists to this day is not 'OMG Missiles OP!' Rather, it's 'All the other weapons
suck.'
A 'recent' (about a year ago) update that buffed Cannons with an inherent explosive effect was welcome, but it didn't empower them enough to make them 'worth it'. Cannons have good range, but they just don't do enough damage. Enhancing them with secondaries...just isn't that good. Cannons seem best used in Cannon+Cannon anti-missile turrets.
Beams hit hard enough, but have very limited range; if Cannons are a really bad rifle, then Beams are really awesome pistols, but therein lies the problem. The lack of range and large power consumption kind of hurts their utility, especialy with missiles, a long range weapon, being the best weapon in the game. I will say that Beams being a hit-scan weapon is nice, though - not needing to lead shots is incredibly helpful. Unfortunately, the long recharge time seriously mitigates that benefit.
Pulse weapons are interesting; if Beams are pistols, then Pulse is punching the other ship in the face, though pulse seems intended to be more of an anti-personnel, defensive weapon. I'd be happy if Pulse weapons were removed from the game, but maybe I just don't know how to use them properly, even years into this game. I've seen plans for 'Skoomer' drones that find an opponent, fly up to them, then spam pulses with tertiary effects intended to debilitate the other ship to death.
TL;DR - The problem with all the non-missile weapons, is that their downsides outweigh their strengths. The reason missiles are the best weapons in the game, is that they're balanced in the first place.
Now, if you want to say, 'But! You can just mod ${WEAPON} in the config files to be better by making the weapon do ${THINGS}!', I say: that's not a good rebuttal, because you're confirming my position that ${WEAPON} has an unfixed problem. Yeah, I can fix it for me, or on my server, but the developers can make that fix the default, and if that fix makes the game better for everyone,
then they should. It's their job, literally.