On this topic, the APA beats out the regular PA (naturally assuming large). The Huge PA beat everything else in total damage beyond 20% resistance, before that huge (fixed) cannon beat it, assuming efficient PA and SR/OC cannon. That said, the pacifiers beat the huge PA in sustained DPS all the way to 70% resistance.
If you can stay on target long enough to take advantage of the faster burst intervals of the APA then yes. The large PAs do 103 damage per volley compared to only 43 for the APA. For the pacifiers all pellets have to hit, and I'm not good enough to get that close consistently. For me my PA setup is the most lethal of the 4 I have, even if I have a large and 2 med SRBs in it and that sucks weapons cap's like it's drinking wine in quarantine. And the heat, poor Gerhard is screaming at the top of his lungs all the time. But that's what I had laying around at the time I put it together and it's nice to delete the shields on many ships in 1 volley. I like the line up, shoot, and reset for the next volley nature of it, not much time on target needed.