And even if you had a micro ohm meter and included the wires, the difference would probably be one in ten thousand so setting the wires to zero resistance is a big help in calculating currents and energy in a circuit.
But there still has to be a way to calculate the energy stored in a looping superconductor, like that one guy said, the energy would be in the magnetic field and the equations can be used for that.
What if you take a superconducting loop with a known current density. While the current circulates, not energy is transferred since the loop resistance is ZERO. But, for sake of discussion, flip a 1 ohm resistor into the loop. Measure the current drop across the resistor... if current is flowing in the loop, then Ohm's law states E =IXR... does this work?