I figured it out, I had the wrong loadout for the boss. Both the homing mites and charge shot don't seem to work on him, neither do assist weapons, so you really do have to spam the regular shot to deal damageI don't think it's bugged, I was able to beat it just fine.
Destroying the wires is actually not mandatory as far as I understood, doing so will give you the chip and maybe make the fight easier. You just have to shoot the boss until he dies.