My experience with missile conquest has largely been to give it a locust SRM to overwhelm/swarm a ship's point defense then follow it up with a harpoon/hurricane MIRV missiles. Point defense AI targets the closest thing to it and this gives you the opportunity to slip the real missiles past its defenses. Harpoons and MIRV's pack enough punch that they will inflict significant flux if they hit shields and inflict significant damage if they hit the ship, if nothing else.
Its a ship where having an officer with missile spec and all the related missile mod's installed makes it a top-tier pick in many situations. Even against remnant ordo's and the elite redacted enemies that hang around the coronal hypershunt.
Agreed. The Conquest is quite suitable for Remnant farming. If you field a fleet of only Conquests or Conquests with frigates, then I don't think enemy PD is really much of a problem. The sheer volume of incoming missiles will overwhelm point defenses. I should give Locusts a try in Remnant farming though, just to see if it does improve things. I would probably replace the Hurricane, so Squall-Locust, since this was also the best combination in testing.
Going a missile heavy fleet is not a terrible idea vs Rem's. Last fleet I ran nearly every ship had harpoons or reaper torpedo's. Mixed in two Harbingers and two Afflictors which is an extremely potent combo vs battlestations cause they will pop the stations shields and most missiles will make it through before the stations shields are back up again. You will need strong forward cruisers though to draw attention from the stations guns, or at least alot of smaller but tougher and faster ships. Omen's work great too as both escort ships and to EMP a target.
The more ships you have, the easier the fight gets really though casualties are inevitable and you might have to play at it a few times. The Conquest makes a great finisher ship, but you really need a fleet comp centered around EMP'ing shields and weapons off.