I tend to go light on HE for the AI, probably 1/3 of weapons/flux generation, but could be more or less depending on what I plan on fighting, more if I will be fighting pirates and ludds, less for high tech and remnants. I then use missiles, bombers and the player ship for killing power. If the AI doesn't die and gets the enemy high on flux, I consider that a success.
Anyway, if 2/3 of weapon flux generation is giving 2 damage/flux and 1/3 of damage is at .5 damage/flux then average output is 1.5 damage/flux. It's more efficient usage of dissipation and capacity regardless of whether you exceed dissipation or not. You can win the flux war at the expense of killing things slower. Usually a good trade for the AI., and not a trade that can be made on high tech ships.
Over-gunning is mostly relevant on low tech ships that can easily fill their entire dissipation with kinetics and still have mounts to spare. They also tend to have lots of missiles mounts for 0 flux HE to back up that kinetic damage and armor to deal with high flux situations better.
On another note, I wish that I could test against ship variants that I've made. The default cruiser load outs are so bad in the sim that testing against them doesn't really tell you anything.