Could try setting ammo really high and see if that does something, too. E.G. Locusts etc seem to have no issue firing at stuff.
Ok, so more feedback here. The problem was 2 things coming together to create a "no fire ever" situation for the AI.
Increasing the ammo from 2 to 8 seemed to help considerably. This makes me think that the DO_NOT_CONSERVE tag is a little misleading because with low base ammo the AI still wants to conserve one or two missiles. Maybe a separate tag for that would help? For some missiles I want the complete alpha strike because it has the most chance of getting through the PD screen or capitalizing the most on an overload, etc.
Second: Unlike energy or ballistic weapons, missile hardpoints don't swivel their firing projectory for hardpoints with increased arcs. This means that any weapon hardpoint projectories that could include missile weapons have to tilt their axis to converge to a point as close to maximum range (hard to balance as you'd imagine if rockets and torps have varying max ranges) as possible in order for the AI to fire those weapons. Adding tags like GUIDED_POOR (merely better... still not optimal unfortunately) or DO_NOT_AIM (100% fine) help if the missile can track, but if the missile is a rocket or torp it has to converge its projectory to be fired or be included in an alternating weapon group. The problem with the second solution is the AI still isn't very efficient with that setting atm:
For instance, the medium reaper with 2 max ammo put into hardpoints set to alternating fire with two total weapons in the group can't even fire enough to reduce the max clip of 2 down to 0 even with a 67 reload time on the missile.
Setting the ammo to 8 leaves the average clip size to around 5 to 6. So not optimal considering the DO_NOT_CONSERVE tag for sure.
Setting the ammo to 8 and making the hardpoint projectory converge around max range for the weapon fixes the problem and the AI empties the clip and kills the enemy vessel.
In this case, its the difference between the vessel losing horribly or, alternatively, if the behavior is accounted for, alpha striking the (weaker) opponent and winning with a supreme victory itself.
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Ok, now all of that said, the above fix is irrelevant for phase vessels. Phase vessels are very unwilling to use strike weapons in general. I had to change a tier 3 dps weapon with minimal flux build up to not use the STRIKE,USE_VS_FRIGATES tag combination in order for that weapon to ever even be fired by the phase battleship at all (Its a large energy weapon).
The long range strike beams (also large energy strike weapons) are fired more often, but at about 1/3 effectiveness over their actual cooldown, reducing weapon effectiveness by the converse amount. This is while the phase battleship hovers at ~15% to 20% max flux, so it's not that its unable to fire the weapon in case that was the concern.
Torps- almost no matter what I do- are either fired at 1/3 effectiveness in the best case scenario where the large weapon with 12 ammo converges to a point for AI hardpoints to fire, or at worst case scenario the group of 4 turret Reapers with 8 max ammo are never fired at all- even within range with either STRIKE,DO_NOT_CONSERVE or STRIKE,USE_VS_FRIGATES,DO_NOT_CONSERVE tags set.
I hope this helps. Let me know if you need more testing to help further narrow this down!
*EDIT*
I tried some more tests for phase ships and it definitely seems linked to their threat evaluation. The phase battleship is much more likely to use large hardpoint (with a high max ammo) torps against cruisers it can easily outgun. It still won't use turreted medium torps against them unless they overload or are already mostly beaten. The DO_NOT_CONSERVE tag doesn't seem to affect the behavior here.
Against a battlecarrier roughly equal in combat strength, it refuses to use torps unless at half health or more. It will also use them (again very sub-optimal to actual reload times) against overloaded ships at equal strength.
If I pilot the vessel myself and use the torpedoes optimal to reload times, the fight is fairly easy in all cases.