Most of the targets I send Reaper Afflictor at do not use omni shields, but have tremendeous armor and hull to chew through, namely Onslaught, Legion, most cruisers, and especially battlestations. Against targets that have small arc, omni shields (like that annoying pirate Venture) I wait until it is distracted by the rest of my fleet, then launch. (But usually, I pass on those and pick off big, tough targets with fixed shields immediately - see above.) In any case, I want them dead immediately, and I do not care if it has less steam than AM Blaster ship. Reaper Afflictors are Ultima V-style glass swords in my fleet, which I bring out to assassinate big, annoying targets faster (or more cheaply) than my conventional fleet can deal with.
Afflictor is not a perfect substitute for Reaper Harbinger, but it can still do most of the cheese against a large chunk of available targets, including battlestations (where I really abused Reaper Harbinger last release, and currently abuse Reaper Afflictor today).
For small fry, I usually send conventional warships or carriers (or Doom) at them, although I occasionally use Harbinger instead (often to conserve CR of my big bad capital flagship).