As was said, Atropos competes with Harpoon because it's simply better. If there was a 10 OP Atropos launcher with 12 ammo, 2 salvo, I would put it on all my ships and would never, ever use Harpoons again. The 2-shot Atropos is a clear upgrade to the 3-shot Harpoon for me. I might not use it if it's too early in the game and Harpoons do fine against unshielded pirates and smaller threats. Or if I simply don't have it yet. Or if my flagship is required to carry a bigger burden, where I might use Annihilators instead and go for longevity.
Manual aim weapons don't have this problem. They are are harder to use, harder to exploit and can't be fired from the rear ranks. Which is why the med Reaper launcher is.. not even that great to me. YMMV.
Remember when the Atropos change came about and people were saying "Omg, they're like Templar Clarents!" That's how powerful that kind of damage paired with high speed is.