"Effective" meaning good enough to kill early-game pirates and pirate bases long enough until player earns enough money to buy superior ships or build his first colony, or collect enough junk ships to kill a bigger fleet (like that very first expedition from a major faction) and steal their cruisers, then use those junk cruisers to steal a capital.
I do not remember stealing Hammerhead hulls from pirates. Sure, it would be great to steal superior hulls from pirates if I cannot easily buy good ships at will, but pirates that are beatable with a starter fleet use Enforcers, Mules, and Shrike (P).
Honestly even with complete removal of missile slots it still will be brocken thanks to its damage amplifier.
Because the other options may not one-shot big things in a single salvo, except maybe four AM Blasters, whose range is short enough to be maybe within the blast radius of an exploding capital. Also, Reapers are great for Quake1 rocket launcher-style splash kills against battlestation segments. Fire boosted Reapers at the wall behind the module, and the module will still be destroyed. Conventional weapons cannot do that.
Harbinger with phase lances or AM blasters is kind of underwhelming even with Quantum Disruptor. It was too powerful with Reapers. With phase lance/AM Blasters, Harbinger is a decent small ship sweeper. I would not use it instead of four Reaper Afflictor against a cruiser, capital, or battlestation. Quantum Disruptor is generally more cheesy than Entropy Amplifier. If Afflictor lost all of its missile slots, I would not use it at all, except as an improvised phase hauler (for marines or loot) when I raid Culann for blueprints with a pure phase fleet.