I really hope you have all weapons get a change like the particle beam change, and not just particle beams! Big guns are way cooler than small ones, but as it currently stands, there isn't much benefit to using them. A beam weapon's dps is its capacitor recharge tech, with no gains from increases in focus size except in the possibility for up to 17% shock damage for larger guns, and the hope of immediately penetrating their armor in a single shot - which is really disheartening. it means any size increase for a weapon over your capacity is essentially wasted, because the probably significantly less than 17% shock damage you've increased is practically never worth reducing your effective DPS exactly proportionately to how much over recharge capacity you are, and then some extra because bigger guns take up more space. And for all that cost, all you do is concentrate more damage in a single area according to your damage profile, which when you really think about it, only is potentially useful on lasers that have nice profiles, plasma cannonades whose whole advantage is being bigger really has no advantage at all. It's not impossible for the extra penetration to be worth it, but it's just feels like such a bad trade off, that it makes researching more than your capacitor recharge tech feel like a waste, meaning you mainly go for railguns (single shot) for the extra 33% damage. Ground units gain racial weapon damage from the size of their beam tech, not the capacitor, even though for the ships it's capacitors that really determine damage, so there's clearly something off here.
Also, capacitor recharge rate being your dps means you want more quantity than quality - which is the same strategy that's good as PD, making it such a no-brainer choice.
You could make it always have the same size, and this would probably be the simplest balance wise, but the idea of bigger weapons taking up more space is too cool to not have tbh. So the obvious thought is, increase damage proportionate to the increases in size, whilst keeping recharge costs the same as before, meaning being bigger is just as efficient a weapon in terms of DPS as a capacitor sized one, but benefits from better penetration and range. That way there is 0 reason outside of being worse as PD fire-rate for using bigger weapons, which is of course great because that's a meaningful decision, and big guns are cool.
The big problem is this means there are now MUCH higher penetration weapons in the game, who's only disadvantage is being worse vs missiles and extremely tiny ships. Though it is interesting that this actually does open up some interesting gameplay funny enough. Past a certain point, your weapons are killing your enemy in one hit, so you actually don't want to be too close, nor for your ships to be too large, meaning you're not going to want to be at close range, which is actually some pretty cool emergent gameplay, as well as maybe giving beam fighters a possible beam weapon niche? Armor combined with speed is good vs missiles, so choosing to forgo armor because of the high penetration environment creates a bigger weakness to missiles. it's just such a choice between what you want to be good at??
But well, too much penetration is probably unacceptable tbh, so what if we went with more capacitor efficient than damage efficient? But well, a rapid fire big gun is silly. Maybe the best balance would be a combination of the two approaches, where it is slightly more damage and fire-rate efficient to make up for the increased weaponsize. Also, it probably shouldn't be perfectly efficient but it's still a bit less efficient to make up for the fact that it's benefiting from better penetration / shock damage profile, so light guns are best PD, medium guns are most damage efficient, and heavy guns are best penetration (but not as bad of a deal as they are now), which is just. . . kind of realistic? You could even make it that unlike other weapons plasma cannonades have perfect damage efficiency for their larger sizes, given that their poor damage profile isn't much of an advantage anyways.
Tbh the true solution might be to just make it proportionate in resource cost efficiency, and powerplant efficiency, DPS efficiency be damned. Yeah its weird for something bigger to be cheaper but I mean engines are like that so. Anyways that's enough thinking out loud. Hopefully you will come up with something, because big weapons being bad is sad :( and it would be really cool if they had a niche as a specialized anti-beam-ship weapon.
