It's highly symbolic from a police perspective. We may see it as some kids who watched too many documentaries playing a harmless prank. But let me rephrase that to put that in the frame of mind of the investigators. "Unknown individuals infiltrated a heavily guarded and highly visible piece of crucial infrastructure undetected. Once present, they defaced the public property by removing two American flags, and replacing them with white flags, a typical signal of surrender. The suspects remain at large."
It's about the symbolism, not the act. If NYC, for all its counterterrorism efforts, can't catch these pranksters, it makes the public safety officials look impotent in the face of real threats.