I have no problem with using AntiMatter blaster Afflictors. The only problem with Afflictors is that as they require skill and some patience and some judgement. Afflictor simply aren't as powerful as a Harbinger. The difference is their ship system. The Harbinger's ship system, Quantum Disruptor means that a ship has to take Harbinger hits to their hull, whilst Afflictor has to hit aim where the shield is not, or have to have good timing. If it wasn't for the ship system, Afflictor and Harbinger would practically have the same playstyle. So the difference is not AM blaster, but that the harbinger is simply better than the Afflictor in any case where you want to kill a ship immediately. As it is, they are close enough together anyways that the differences can be regarded as fairly minor.
I've used plenty of different Afflictor load outs. Generally speaking, for the Afflictor, 2 AM blasters is enough. 3 is too many as there isn't enough of a flux margin to approach, fire all three AM blasters and retreat out of long range fire completely safely. The other two forward mounts can be LAG if you want a reliable way to go through armour after breaking down a shield, and the turret can be ion cannon. Or they can be reapers.