True enough - having or having not the Imrecs really makes difference out there. But... if a Tarsus (which is the most primitive and outdated design) can change its loadout, why Hellcats and Thunderbolts, which are much more fresh - can't?
I'm not sure if it's known that Tarsus is older than Hellcats and Thunderbolts for sure- a lot of the WC3 fighters from my understanding are relatively as old as the hills too.... and just because one can do something within the game universe (like load every hardpoint with ImRecs, or Torpedos, or whatever) doesn't mean it's a great idea from a gameplay standpoint.
It makes more sense to allow the player to pick his loadout in a game like privateer, for two reasons- first, because financially speaking, he's responsible for every missile he fires, so at least there is an incentive to conserve (unlike WC3-4, where you could pick the same missile every mission and never run out). Secondly, Privateer also did not have a defined mission structure like the other WC games, nor were you operating off a carrier featuring several different types of fighters with defined mission roles- there was a linear storyline in Privateer, but you could follow it at your whim, and your one ship had to be customizable to handle whatever type of mission you could decide take, because you (or your colonel) couldn't assign yourself to a dramatically different ship for just a short series of missions- In Privateer, your ship had to be able to reconfigure to deal with missions varying from exploration, escort, trade, pirate whacking, or striking Kilrathi military targets. Hence, Privateer's nature required allowing the player to customize his ship.
Personally, I wouldn't mind allowing customization of fighter loadout in a reimagining of Armada- you basically manage the strategic and logistical aspects of a carrier group (including fighters and capital ship assets) with the option to fly off your carrier after you give your task force commands to follow in the moments before engagement (e.g. Carrier hang back and offer logistical fighter support, all cruisers close within gun range of enemy destroyers, all medium fighters protect cruisers, all light fighters protect carrier, etc.)- kind of like a hybrid of Armada and Rainbow Six. Again, it makes more sense here because A. the gameplay is open ended (you're in command of your carrier group's missions), and B. you face logistical issues in having good missiles in the future if you load all your good missiles up for fighting in a single engagement.