That is basically what a protection diode is - except they do not use zener diodes. They have one diode connected to ground and one to VCC. If the voltage drops below ground, one diode conducts clamping the voltage to ~-0.7v. If the voltage increases beyond VCC, the other diode conducts and clamps the voltage at VCC+0.7v. This is effective when dissipating a small charge that could potentially be at a high voltage - think ESD. But if you have prolonged current the diode will blow and short.
So you have a short (blown diode) but you still have a significant amount of energy to dissipate. This results in a large current that will cause the diode to physically explode or possibly blow a trace. USB data lines typically use very thin traces and can not conduct much power. If a trace goes then USB is screwed but the rest of the computer will probably function correctly. If the diode explodes your protection is gone and the high voltage will now cause all sorts of damage.