That's a valid point, but I think it's a gameplay limitation more than anything. (Nearly) all races have an unlimited number of ships in their spheres of influence. Amusingly, it's unclear exactly how many Ur-Quan were destroyed:
The description of the losses suffered by Ur-Quan fleet varies from source to source: the Yehat assert that nearly thirty percent of the entire Ur-Quan war fleet had been destroyed, the Melnorme say that over a hundred Dreadnoughts had been caught in the miniature nova and the Shofixti allege that there were hundreds of Dreadnoughts destroyed. According to the Chmmr, this act also resulted in the Kohr-Ah fleet vastly outnumbering the Ur-Quan, which gave them a very significant advantage in the Doctrinal Conflict. Fwiffo, on the other hand, states that the blast only destroyed "dozens of Dreadnoughts", implying that a relatively small number of ships were lost.
I think we can trust the Chmmr and the Melnorme, and perhaps the Yehat.
Despite that crippling blow, the two fleets are closely matched. And the player's ship, despite being an oddly modular tugboat, is nearly invincible once fully upgraded with Melnorme weapons technology. It could easily destroy hundreds of Kohr-ah per month, shifting the balance of power back to the Kzer-za.
That's my speculative headcanon. And despite their reasons, a Kzer-Za victory is hardly ideal anyway.