I am playing this game since "hey hey people" reviewed it, on day one, and this was also confusing to me.
Just registered on this official forum and I am reading the pinned topics, one is just about that.
In short, Ai doesn't care it the weapon is in autoshot or not, if you switch controls to na AI controlled ship, all weapons with autofire will be turned off, just the PD ones will be on autofire.
The ai will shot all groups, even at the same time, if he has enough free flux for that. But the AI will NOT alpha strike!
After reading the pinned threat, now I know that the AI will not fire a group with it costs more them 50% of the available flux pool, so, placing all antimatter blaster on a single group and linked fire, will not work, because there is not enough flux for them to fire it.
So, for AI SHIPS, if one group uses more them 30% of the total flux pool, like a Radiant with 5 tachyon lances (something I did), it is better to split up in 2 or 3 groups those tachyon lances, so it shots alternating.