I did not use missile hullmods because I did not have enough OP left to afford them. I already had to leave the two medium energy mounts (which could have taken Ion Beam for shield pierce or more burst PD) empty to get everything else I wanted, and if I wanted the hullmods, I would either had to give up all of my burst PD or Hardened Shields, which probably would have hurt Conquest defenses too much. Conquest wants some PD to avoid overusing its shield, and Conquest needs either Hardened Shields or high capacitors for its shields to withstand some damage. Conquest with Hardened Shields and/or high capacitors can shield tank decently enough despite terrible efficiency, enough to match and trade blows with Onslaught or the like. It probably wants Resistant Flux Conduits to speed up venting too because venting speed is not quite fast enough with max vents alone. Deep flux pool plus inefficient shield is not a good combination for venting.
That is a reason why I like Locusts, at least as good as finishing off ships as MIRVs, but cheaper, easier to use, more reliable, and more ammo. It cannot strip armor of bigger ships very well (although it will strip armor of small ships well enough due to overwhelming damage despite fragmentation), but I have guns for armor stripping, and then Locusts can pile on the hull damage very fast. If I had enough OP to afford Expanded Missile Racks, I would use it for Locusts and nearly spam them for most of the fight. Locusts are the Needlers of missiles.
If I think I would give Conquest to AI, I would not mount MIRVs because AI wastes them frivolously. That would leave quad Harpoon Pods (if Locusts were not an option). At least AI is a bit wiser in their use.
Speaking of AI stupidity, I probably would not mount Sabots on lance Odyssey if I might give it to the AI. AI tends to use Sabots sub-optimally.
Remember, I am testing with unskilled ships. In campaign, I am well aware that Loadout Design 3 is a top pick precisely to mitigate stingy OP totals, and it is very close runner-up to Electronic Warfare #1 as the best perk in the game for everyone, not to mention other skills that make ships better.
Neo Missile Specialization is kind of mediocre, a pale shadow of old Missile Specialization, nothing to be more afraid of than unboosted missiles. Most of all, it is a classic case of pay one point in Officer Management to get two more goons who can get it and more instead of you. If player will rely on a fleet for most fights, better to spend one point for two guys who can spam missiles instead of wasting three points yourself.
As for Conquest weapons, Gauss Cannon seems more useful against small ships than Mark IX. Sometimes, AI does not bother enough to dodge, and Gauss will hit and put a ton of hard flux on frigates (or overload outright). If Conquest would fight only big ships (and no Paragon), mark IX would be better for efficiency (or for AI use), but Gauss (on one side only, used by player) seems more versatile despite being a pig (but that means no Ion Beam because that is too much of a flux load with other flux hogs).
On the conquest, for instance, not fitting ECCM, EMR and MIRV/Harpoons is criminal. And its pretty close on the Onslaught and Legion.
For Onslaught, this is a case where I prefer Converted Hangar and some fighter wing in place of missiles if I want regenerators. If I want burst damage, I gravitate toward Annihilator pods due to less all-or-nothing nature of Harpoons.
As for Legion, I think it is almost criminal if it does not use at least three of its composites for flak, at least if it is configured for brawling. No flak and Legion's defenses are very poor. At least with flak, it can stop things in front of it (less dependence on shield) or the sides, and I do not need to fill all small mounts with Vulcans. Besides, if I really want missiles, I can use bomber wings on Legion (although Astral is better at bomber spam). If Pilum spam was still as effective as it used to be, I could see keeping Legion away from battle and lob Pilums non-stop. Aside from flak, any remaining composites go either to Heavy Mauler or (more likely) Heavy Needlers. Light Needlers in smalls would be ideal, but they are too rare, and Legion can substitute those with much more common Heavy Needlers in a pinch.