EMP protection is not as easy as all that. For electronic devices, the best bet is to keep a backup unit in a steel box. Otherwise any wire, long or short, or wire like conductor in the EMP cone will develop a serious potential in it.
It is so difficult to harden electronics to EMP that the Soviets put tube based electronics in their fighter aircraft, as tubes are less vulnerable.
For the Iranian nuclear program which is reportedly well below ground, EMP field strengths will be significantly attenuated by the ground. The main risk of high currents will be via power and communication lines. I don't know what precautions the Iranians may have taken. If external comm's lines from the tunnel complexes are fiber, the principal EMP risk will then be via power lines coming from topside power plants. This powerline surge risk can be mitigated against.