Disclaimer - I'm not exactly an expert on ElectroMagnetic Interference (EMI), but I do deal with it (basically working with the people who
are experts to make sure my engine systems will operate properly in a given EMI environment).
But my understanding is that the current regulations regarding Lightning and HIRF protection provide more than adequate protection from EMP. Basically, if the EMP source is close enough to overwhelm the existing protections, the blast will be a bigger problem than the EMP...
Note also that while the HIRF/Lightning regulations are fairly recent, aircraft certified in the 1980s were covered by "Special Conditions" related to the EMI threat, and the requirements in those special conditions are not a whole lot different than what ended up in the regulations (principally 25.1316 and 25.1317).