I agree that RNG dodge mechanics are not ideal. It's one of those cases where realism != fun.
As for certain weapons not being capable of hitting and therefore not targeting fighters, I've been barking up that tree for a while. Long story short, there is a cadre of players that really enjoy the 2D arcade-style hybrid uses of assault weapons and consider PD weapons as mostly anti-missile.
Personally, I dislike it - though not because of immersion in this case. I dislike it because of the inherent balancing issues a hybrid system causes. I saw an interesting analysis of some of the bloat design issues the original Guild Wars team started to go up against after releasing their third campaign. One of the big things that people at the time were worried about was separating out PvP and PvE skill definitions. A lot of people thought that route would A) be very confusing to new players trying to do both and B) not actually solve the balancing issues that came about from a skill being useless in PvE and broken in PvP (or vice-versa).
As it turns out, ANET was able to thread the needle very well and the change was immensely popular. The reason they were successful was that they kept a limited number of "sliding balance mechanisms" such as cooldown, cast time, etc as the way to separate the skills between the two game types. This meant the core skill design mostly stayed the same between each version in the vast majority of cases.
To bring this back to Starsector, Alex will likely start running into the same kinds of considerations using the hybrid weapon system. Take the Devastator. As people have already said, it's not great as an anti-fighter weapon but deals with frigates and destroyers very well. So, think about it: if the weapon is changed to be more accurate to its role, it has to be done very carefully or it will get
even stronger as the anti-frigate option. Because each weapon can essentially serve multiple roles - at least when under manual player control - each change to a weapon cascades into multiple areas of combat. Even if the AI can't always leverage a change to their advantage, then you're dealing with a situation of player power creep - which already has to be carefully monitored.
Some players don't want their hellbore shots to be stopped by fighters, and some like using it that way and want it to remain an option. Ok, so give the hellbore passthrough (it might already have it I can't remember) and that solves the problem right? Maybe. It could also make the hellbore too flexible and become a catch-all weapon. As we can see, PC already kind of is.
The main consideration of the PC is high flux generation - not its combat performance. If the big bad anti-ship weapons are also useful in stopping bomber waves, imo they are too strong. Simply having high flux generation won't matter to the player as much since they will just find a ship that can handle it.
TLDR: I don't like anti-ship weapons also being useful against bombers because it limits the overall design space and makes balancing that much more difficult.
I also don't agree that weapons like the plasma cannon are actually amazing against fighters. Sure they shred bombers flying slowly in a straight line right at you, but fighters that are moving quickly in strange directions are not reliable to hit with PC, unless there are simply so many of them that it is hard to miss. PC also costs a ton of flux to fire which is not what you want from PD. Accurate beam weapons are much better in that scenario (agile fighters moving evasively) IMO.
Fighters are only a real threat to big ships when there is a lot of them. Which is exactly when Plasma is good. Beams and PD are for mop up against the few fighters that survived approach vs Plasma. Unless we are talking about 4xTL Paragon, which is comparable to Plasma against fighters.
So looking at this from an AI perspective - there is no clear road for good AI behavior when you consider this analysis. Sometimes PC needs to be fired at bombers. Sometimes its really bad for the ship to do so (nimble fighters at close range) because it will generate too much flux. That sounds like a balancing nightmare to me. I think it makes the player too strong because they can make these calls and the AI will never be able to keep up. I also think it's the primary reason that players complain about fighter spam: they aren't dangerous in low numbers and break the AI in large numbers.
One way to perhaps solve this
without what I know some of you consider "arbitrary combat rules" like a weapon being unable to hit fighters would be to change bomber behavior. Essentially change bombers to act more like fighters. They maintain full speed - they try to dodge over moving in a straight line - and they don't clump up. Instead, they try and coordinate an attack from multiple angles to give weapons like the PC a harder time. If that can be accomplished, I think true strike craft balance can be achieved and some wings won't need the padding that they currently have in order to not be invalidated by large weapons. Even still, that change creates balance complexity in other areas. For instance, how realistic will it be for bombers to coordinate an attack that way? If they end up trickling in to attack instead of acting as a spread out "wave", then the power of the strike is greatly diminished.
Idk, to me it seems straightforward to separate out the design space into more concrete roles and let hybrid role weapons be a niche exception rather than the rule. It makes balance so much easier. It may seem arbitrary or hard to communicate to players on the surface, but I think that is far more easily solved than the alternative considerations I've mentioned. It can be done visually, descriptively in the stat card and weapon blurb, and mentioned in the tutorial. Eventually, I think it would become rather intuitive to the player - especially if Alex tore a page out of Guild Wars' book and kept the types of weapons that behaved this way mostly thematically identical with a few balancing sliders.