While true that high flux interferes with offense, AI drops its shield more now and will take hits on armor. AI also vents more. It is not so easy to stunlock AI as before. If player relies on kinetics alone, it will take a long time to kill some ships, and time is not a luxury some ships have. One time, I tried all kinetic Hammerhead against SIM Dominator, and barely won before CR degraded to critical. Another test, with mixed arms, and the fight finished much faster.
Because AI is also cowardly, it is a good idea to finish off the AI when they leave themselves open before they recover and kite-and-turtle again.
Similarly, if you are forced to trade shots with a dangerous enemy bruiser, you may want to finish off the enemy before it does the same to you.
Also, Warthogs are armed with Mortars, and they wreck targets they swarm (due to poor shield coverage and/or dumb AI that lowers shields). Broadswords are similar to Warthogs except they use LMGs instead, and they do not kill targets very quickly.
Yes, relying on HE alone is not a good idea, especially since the skill that has the perk that lets armor shrug off kinetics better also has the perk that lets shields shrug off HE better, but relying on kinetic alone is not as good as it used to be, given AI improvements and skill perks.
Personally, if my ship can use ballistics, I favor kinetics to HE by 2-to-1, although in 0.8, I sometimes go half-and-half. Before 0.8, single HE and the rest kinetics would be fine. Today? Probably not as useful.
As for missiles, I only mount them if I can afford them or have nothing better to spend OP on. If my ship is starved for OP, missiles are the first to go to free up OP. For most of my large ships, Converted Hangar and a wing of fighters take the place of missiles.
That said, at least half of my ships are carriers because fighters force fights. Other ships play keep away and stall until CR decays to zero. Does not matter too much what ships are armed with if they avoid fighting when they cannot swarm a target. All the more reason for non-carriers to use mixed arms to kill targets fast when AI makes a mistake and provides an opening.