"One theory states that they use the transphasic cloak technology to penetrate a ship's hull, and detonate within the ship, but another says that transphasic torpedoes are based on generating a destructive subspace compression pulse. Upon detonation the torpedo delivers the pulse in an asymmetric superposition of multiple phase states. Shields can only block one subcomponent of the pulse. The other subcomponents deliver the majority of the pulse to the target. Every torpedo has a different transphasic configuration, generated randomly by a dissonant feedback effect to prevent the Borg from predicting the configuration of the phase states."
Although I've not read anywhere else about the second explanation of their function, I'm willing to explore that as a possibility. Until then, we at least know of transphasic cloak technology and that would be the best explanation of what came out of those experiments.