The referenced April 1 New Scientist article serves up a deliciously confused and obfuscated perspective that seamlessly entwines EMP & Electronic interference as though they were one. One may see it most clearly as a very indirect spoof on the Global Warming froufrou, IMHO.
Lest someone take pocket-EMP generators on as a challenge, one will not attempt to discuss specifics of electromagnetic mischief in this forum, other than to point out that EMP efects typically derive from very High-Energy processes and those, or their sources, generally are quite conspicuous by their presence and support needs, so not well-suited to covert and portable applications done on a budget.
Along with simple, ancient methods like shielding and proper technical design of aircraft systems, the property that makes vehicles and systems most successfully resistant to attacks of various sorts is "Robustness" in the way that critical component, subsystem, and system failures are handled when they occur - whatever the reason. Early aircraft had little or no redundancy and hardly any ability to endure critical failures, but they did not have very many components. With advancing time and especially growing virtuosity in use of electronics and computing to manage things at the nuts and bolts level, aircraft systems using billions of working components are increasingly made to "fail soft" when problems occur, so that operations may continue in a degraded but adequate manner after even very serious problems. The human crew members are, of course, the ultimate fail-soft tools in the program.
Newer aircraft are likely to be much more resilient than older ones - except in cases where thicker pieces make the critical difference. New technologies may have other vulnerabilities, however, and may have different unperceived failure modes that can make for new risk exposures. Very electronic and very digital aircraft may prove more vulnerable to random operating errors and other sorts of internal functional confusion caused by external means and threats, by operator errors, and also later in life by accumulating effects of incomplete or inappropriate maintenance.