The reason for this is that the Endeavour is designed to be a heavily armed warship, but not a ship that is meant to engage in direct combat with the Flying Dutchman or the Black Pearl.
* The Flying Dutchman: The Dutchman is a ghostly ship with supernatural abilities, including invulnerability to conventional weaponry.
* The Black Pearl: The Black Pearl is a fast and maneuverable ship, and while it has some firepower, it's primarily designed for speed and stealth.
Instead of engaging in direct combat, Beckett uses his ship to capture the Black Pearl, which is captured after a lengthy chase. The Endeavour then uses its superior firepower to overwhelm the Black Pearl's crew, taking the ship and Jack Sparrow as prisoners.
The Endeavour, while powerful, was designed to dominate the seas through sheer firepower and control the flow of trade, not to directly engage in combat with other ships.