imo missiles are the best weapons in the game. They will insta-kill anything with shields down.
Harpoons lose effectiveness against cruisers/capital ships simply because you can't unload enough in a short enough time. Use reapers instead.
If you want to see the power of missiles, try using this Conquest loadout: cyclone reaper launchers in the front, heavy autocannons/hellbore cannons on the side slots, 8xPD lasers, 2x heavy burst lasers, stabilized shields, hardened shields, advanced turret gyros, dedicated targeting core, rest capacitors, missile side slots empty. Set all weapons to autofire except the reapers. Elite crew helps keep flux down.
You can kill any capital ship/cruiser in less than 10 seconds typically with this loadout (exception is the Paragon with its anti-strike weapon fort shield). When you see an enemy capital, engage maneuvering jets, ram them, fire torpedoes at point blank, turn broadside. If they are somehow still standing, stay in your point-blank broadside until the maneuvering jets and reapers recharge, then face them again and launch.
You can do this to kill an Onslaught and take no damage (as long as you can briefly distract any escorts). Vessels of cruiser size and below pose no threat unless you are massively outnumbered (hellbore+HAC+reapers will overload and kill anything in range). Gets old pretty quickly, but is extremely effective.
Personally, I think the Conquest could use a bit of a nerf. It seems a little OP to be able to zip around the map like a frigate and be able to one-shot capitals with your torpedoes.