Okay, I’ll try to be as philosophical about this as I can. I’m not really sure exactly what GBX had in mind in all the cases where they elected to maintain RNG, but, the biggest red herrings in these cases I believe are the bombers and the Vaygr trinity cannon.
Let’s take the Vaygr trinity as the primary example. We’ve probably all seen how this cannon functions versus frigates in classic HW2. It fires three bolts into a frigate blob and, in my experience, one-shot-kills about one frigate out of three. Sometimes more, obviously, with the whole RNG thing, but usually about one in three. So now we have ballistics. Frigates are slow targets, trinity bolts are mighty speedy, and though frigates are tougher now than they were in HW2C, it’s not a stretch to think that the ballistics system would turn the roughly 1/3 pattern into a pretty consistent 3/3. That’s 3 dead frigates every time (assuming it still only takes a single trinity bolt to silence a frigate, which it might)… the weapon is now roughly 3 times more deadly in that respect!
It’s relatively the same for bombers. If someone were to make the mistake of putting a wave of interceptors in aggressive tactics to kill a wave of bombers, those bombers, if they had ballistics, would be one-shotting those interceptors into oblivion, completely reversing the intended balance between those kinds of units.
So it’s hard to say exactly what weapons you should use which system for (without having benefit of having played your mod as extensively as HW2 itself), but at least hopefully this gives you some frame of mind about how to consider the question for yourself. If there is some crucial reason you need to have a weapon miss sometimes or often, then it should probably be RNG, elsewise a very slow projectile. If not, as far as I can tell, you might as well always use ballistics.
One other observation though before I completely conclude - if you’re not planning to change the way the game is balanced substantially, production ship point-defense guns should probably all remain RNG too. I’ve noticed that the way things are now, a Carrier can one-shot most fighters, so if you were to sphere attack a Carrier with your fighters, they will ‘pop-pop pop pop’ right out of the sky before you realize your mistake. This is rather quirky because you as the fighter-commander are making what seems like the logical choice for killing the Carrier as quickly as possible, with no way to know ahead of time that what you are actually doing is sentencing all of your fighters to instant death. This was never an issue before in HW1, because not much of anything other than an ion frigate could one-shot fighters, so they would last long enough to beat up on the Carrier before suffering significant losses. The sad thing is that the ballistics system doesn’t play really friendly with fighters that have tissue-paper armor. So keep that in mind when you’re deciding whether a particular ship is meant to be a very effective fighter killer or not.