Well, one has to take into account that starsector takes place in a region of space cut off from the outside worlds, all gates have died, and since then the level of technology and education has steadily decreased, replacing or buildings new ships and weapons is next to impossible, most ships you see(that isn't junk) are ships that have been around since the day the gates died, and new ships and weapons that are built are junk at best with the occasional diamond among the rocks, and the markets reflect this, in reality, the longer your playthrough lasts, the
worse the markets are going to get, or atleast that is the idea, your trying to survive in a dying universe.
To tackle the question about weapon sizes and general balance.
Rarity and cost, is not a valid way to balance things, I can get the weapon one way or another, I can mount it, its overpowered, and your back to square one.
Missiles in particular are extremely strong, they do HUGE damage with no drawbacks, if I have said weapon, but bigger, whats even the point in mounting something else?
Why bother with a large reaper launcher that is special because it fires 2 torpedoes instead of one, when I could mount a large harpoon launcher that does the same damage, can track a frigate, has longer range, and more ammo? even if it costed more OP? this would also make the MIRV useless, because this is the intended role of the MIRV, to offer a large slot solution to smaller or crippled ships at range.
Having a large variety of different weapons at different sizes gives each weapon a value and makes them interesting, the mauler is considered the best medium weapon, if there was a small and large mauler, not only would the medium mauler lose some of its value, the large hellbore would now be pointless and so would the light AG together with a bunch of other weapons that are good because weapons like the mauler, is a medium mount exclusive.
And lastly, having to many options isn't good either because at the end of the day, im always going to pick the best weapon I can get, if I have 100 different weapons to choose from, and only 10 of them are worth mounting, why do the other 90 weapons exist if nobody would ever use them?
If you dislike the way vanilla does things in its current state, there are more than enough mods out there to spice things up.
Spoiler
There actually aren't that many ballistic/energy weapons with a strict linear progression across all the sizes. The only unambiguous example is Light AC/Heavy AC/MkIX AC, although the needlers and Burst PD/Heavy Burst/Guardian PD come close, and Railgun/HVD/Gauss is a bit further away.
Spreadsheet!
Based on my groupings, missiles have almost as many loosely grouped linear progression chains as ballistic and energy weapons do.
Second, why are most ships and weapons, even the basic ones, so god damn rare and scarce? Doesn't that defeat any strategy behind building up your fleet most of the time? If you don't save scum every time you lose a ship, or every time a large fleet catches you with your pants down right as you jumped to/from hyperspace, your fleet will be composed of just random crap that was available. I get it when it's just early game, having to be scrappy at the early stages makes sense, but that should stop once you join a large faction and have access to military markets. Your fleet is just glued together randomly without any strategy because the "take what you can get" is pushed to an extreme even after hours and hours of grinding.
I don't know about vanilla, but in a modded game I can usually find what I need (though Prism Freeport and compulsively hoarding every weapon play a big role).
Generally speaking, I think it's fine that you don't always have the exact ship you want available. It's easy enough to get a decent approximation for the role by kitting out a similar ship with the right hullmods and weapons anyway.
The future feature that will cover this is the industry update, which will presumably allow the player to make their own ships as needed.
and indeed as above post says at the end because god dammit i take to long to type (x_x)
industry will allow you to a reasonable extent, get the things you want.