I agree with the former statements that all available crafts would be used to defend Sol against the attack launched by the Kilrathi.
Plus, after the incident the construction files may or may not have been reviewed and found obsolete due to its flaws, price - or - newer technologies developed.
Think about it this way: I magically beam you through time to an American aircraft carrier in 1943. You see Hellcats, Dauntlesses and Avengers. Does this mean that there are no Mustangs, Thunderbolts, Spitfires, etc. anywhere? That they were all retired because you know from history that there was a major battle a month earlier? Of course not!
That would probably explain the suffixes in the WC3 fighters --Hellcat V or Thunderbolt VII. Probably they are iterations of older (but possibly effective and tested) designs updated with new technologies and adapted to meet both latest Kilrathi designs and changes to the Confederation doctrine.
The Roman numerals designate a new (and unrelated) spacecraft design; think the P-47 Thunderbolt versus the A-10 Thunderbolt II. The Thunderbolt VI and the Hellcat IV would most likely be from some previous era.
It is on topic about the Morningstar, as costs, both production and maintenance, would have been a decisive factor to the authorization of its mass production.
Those are usually things that happen at the start of the process. In Special Operations 2, we're seeing the end of a years-long process that began with the Navy identifying the need for a heavy strike fighter. It would be odd to commission, fund, design, prototype, production prototype and then combat test a ship you've decided you need for your ongoing war only to decide that /now/ it's too expensive.
And we see the Morningstar after Special Operations 2! They're in Academy (the game) which is set the year after SO2 and Confed is now training pilots on them in the sim. And the manual says they're currently Confed's premiere capital ship destroyer. And they show up years later, too, as one of the surplus ship types in an ad in Star*Soldier. There were definitely more Morningstars!
(And you also have to ask: why would we need there not to be Morningstars after SO2--what piece of information suggests that in the first place?)