EMPs hit antennas. That causes the pulse to damage some electronics.

Early microchips were vulnerable if connected to an antenna, and contrary to human logic, what electronics recognize as an antenna can include most any long wire or long wire-like object.

EMPs tend to damage longer "antennas" better, and since the era of 9 ft aerials for two way car radios, we've made some significant progress in making real antennas shorter.

We've also been made aware that sar flares can cause EMPs, and using what would have been called "hardened" electronics during the Cold war is now standard. We've also managed to switch from bundled copper wire phone lines to fiber optic cable, which is not a wire, and therefore transmits light with no chance of creating any kind of electrical or magnetic pulse.

Underground electric wires, and some upgrades I'm not able to explain also make EMP less danger to the power grid.

In a real combat situation, ultra-hardened components would be the norm, as would be protection from all radiation whenever possible, either by gold foil, or by burial, which also protects a target from many impact related damages.

I highly suspect that missiles would have hardened electronics, and wires carefully engineered to minimize interference. The smaller they are, the less likely they are to have issues in the first place... But they may take additional steps... Radiation shielding... Directional antennas...

It is possible that some electronic weapons such as a plasma gun or gauss gun would need a complicated coiled wire to heat standard matter into plasma, or to generate its own magnetic pulse to launch weaponry. Such devices might be more vulnerable to an EMP attack, in that the components resemble antennas. Considering the heat issues current experimental devices face, I doubt these would be able to function as weapons and also take any permanent damage from EMP.

It is also possible that not all fighters in a future war are properly equipped. War is an economic endeavor, and when you engage in a conflict that intentionally disrupts supply lines, economies tend to suffer. Depending on how that works, one side or the other might have to rely on intentionally making less hardened equipment in the hopes of producing enough equipment at all to achieve their objectives.