The bomber is designed to take down capital ships. In order for the bomber to accomplish that task, it needs a Supernova. Thats it, there's nothing else to it.
To expand more upon that point: In order for a bomber to fulfill its purpose, its weapon system must be able to down the shields of a Battleship, and perform significant damage to its hull. If bombers were unable to penetrate capital ship shielding, they would be utterly useless.
