For the first two seasons, Enterprise used spatial torpedoes as its matter weapon and phase cannons as its energy weapon. Then, for S3, it switched over to the same phaser/photon torpedoes weapon set that would persist until quantum torpedoes were introduced 220 years later. Problem is, there was no inkling that the Federation was developing or even had knowledge of photon torpedoes before then. The Vulcans might have had such technology, but given their adamant opposition to Archer's mission, it's unlikely that they would share it. The Klingons used them, but Archer and his people were the only ones with hands on experience with a Klingon ship. They had little opportunity to reverse engineer the weapons, especially given that they fired them all. And besides, there's no evidence that they were involved in the new armament's development. The Vissians use the technology, and they were willing to share information, but given that Trip caused the death of their cogenitor, it seems unlikely that they would upgrade Starfleet's arsenal. So... where'd Archer get photonic torpedoes?