For the small slots I prefer either Harpoons (for the range and guidance) or Reapers (for the damage) when it comes to HE missiles, but the difference is fairly minor: if I have to make do with either Hammers or Atropos, they still do the job ok (and despite their short range, Atropos have superior speed, guidance, and hitpoints compared to harpoons, so for a close in brawler they are better than harpoons, they just don't gang up as well).
But for the large slot, the Hammer Barrage is far more dangerous than the Cyclone Reaper while also being significantly cheaper. Hammer Barrages reload very quickly, so have more than double the damage output. The tradeoff is ammo: Hammer Barrages run out much faster.