Wasn't the Macross woefully low on resources through much of the war? I mean yes, the ship DID have its own manfactoring capibilities, but seems reasonable, given the size of the Zentran force, that losses probably outstripped replacements.
To my point... As stated earlier, the -1D HAD weapon hard points, and I'm sure it could handle itself in a fight as well as a single seater (at least in space.) It would make sense that the crew would press these trainers into service to shore up and major holes in their depleted squadrons until new fighters could be produced. That MIGHT explain the -1D's limited combat experience.