You forget the political uproar which would come with a massive refit to quantum torpedoes. If the federation would arm every ship with quantum torpedoes, they'd initiate an arms race with the romulans and klingons who would feel the need to invent more terrible weapons to stay on par. Being that the federation are explorers and the weapon was originally a weapon deviced to fight the borg with, we can assume it is more likely distributed to starships on a special occasion or is accessable only to captains with a certain level of authority.
- USS Enterprise: Flagship, may encounter the most dangerous of situations where quantum torpedoes are required.
- USS Defiant: Invented to counter the borg, quantum torpedoes remained on the ship, perhaps a wise choice for the gamma quadrant's potential dangers and later as a weapon against the dominion.
- USS Lakota: We can only speculate if the Lakota was armed with quantum torpedoes for dangerous missions or if Leyton had ordered such to have superior firepower if anyone'd try to stop his coupe.
While memory alpha says the weapon was deviced to replace the photon torpedo, they've provided no source of how they came to that conclusion.