I have perused the forms and sadly have found very little in the way of weapon discussion outside of mods. So as it pertains to vanilla I would like to see the following,
and while this does sound very demanding I apologize I do not mean it to come off as such.
Now before we get into it I would just like to reaffirm that in my opinion this game is freakin' awesome... And now back on topic.
Some ideas that I think would be awesome to see in the game.
Module weapon systems: first off I started playing during the current version of the game (which is 0.14.2 point to I believe) which gave us access to the real gun mechanic the first and hopefully not last of a modular weapon system. I can see the ions beam weapon being replaced in the future by modular weapon system allowing the range of the weapon to increase cuz and lets be honest after this game does gravitate towards bigger ships. Some Infact getting so big that it starts to get difficult to see the whole ship and crew doing there job. So I guess this section is about weapon power, and range extension modules. To that end...
Rail gun: range extension module... All I can think of for this gun. And yes even with range extension their should be a max range cause shooting across map at enemies you can't see is cheap.
Ion beam: replaces the current six/eight segment block with control block, emitter, range extender, and power amplifier blocks.
MRV: yes a room that creates and launched a late missile with more missile that are to be launched a few seconds after launch.
Now onto what I truely believe this game needs. Fighters/Drones. This idea may upset people but when it comes to this game you can't build a fighter or carriers to house these short range piranha. I will admit that the way this game is currently the smallest ship that is buildable is a frigate/corvette. I think that is fine when starting, but once you get into the larger battleships it would be nice to have more options available strategically (longer range/stronger weapons, fighter screens, ECM, electronic warfare to shut down random doors for 1-3 seconds, boarding craft can be an extension of fighter, and 360 degree rotating turrets... To name a few). The fighters could be made using the same ship editor but instead of relying on crew they rely on automation to supply the engine and control room (cockpit) with power. Using these components drastically reduces the available block count preventing frigate and battleship size "fighters". Lastly the fighter can only fire it's weapons not reload them and requires a "path" from the "cockpit" to all other components in order for them to function properly.
Fighters will require crew to pilot them.
ECM: has the potential to see missiles back at the opponent or just turn them away.
Electronic warfare: is like ECM but only starts to happen when in visual range and will be naturally part of the control module with specific separate modules used to prevent or cause more problems. The higher your defense the less problems with door and moving walkways likewise the more attack the problems caused to the opponents crew.
Turrets: these could be trick but would be considered a modular component to the above mentioned modular weapon systems (not missile). Instead of the usual emitter or end piece you would place the turret and it becomes the appropriate end piece and there are rotation speed modules that can be used to increase turret speed.
If by chance you don't like the 360 turret then how about only allowing 45 degrees of rotation for each side a control module (of the same type is attached. This would allow large ships to be far more threatening than smaller ships while also giving them a much-needed boost to fire power.
Boarding: armoury block and a boarding pod block. While I am hesitant to put this idea out (though no entirely original I'll admit) would be interesting to see boarding battles because those little guys don't have enough time worry about. Then again the invaders could be drones meaning it would just be a different ammo type factory.
That's it this has gone longer enough thanks for reading and please leave a comment. To all those who had similar/same ideas please lay your claim to them an if you wish expand on them as I with this post the embody all of our weaponization desires.