"Energy-based" is rather broad. I'd say a photon torpedo is just a fancy projectile. Trek seems to treat physical projectiles differently than energy weapons. For instance, the Borg will 'adapt' to phasers and create shields, but you can still shoot them with bullets or stab them.
A phaser beam is concentrated energy used to overload/overheat the target. Something like an EMP or stun-gun. But at its core, it's basically an electrical current. Shooting an electrical current at something that converts electrical energy into deadly radiation seems most unwise.