For the purposes of this question, let's use the definition of nanotechnology from the tag wiki excerpt: "technology that works with sizes of less than 100 nanometres".
An EMP can vary in frequency range, but Wikipedia gives "DC to daylight" as excluding infrared and shorter wavelengths. It also gives the range for infrared as 300 GHz (wavelength 1 mm) to 700 nm (frequency 430 THz, or 430,000 GHz). It also states long-wavelength infrared as having a wavelength of up to 15,000 nm, which corresponds to a frequency of 20 THz. (Remember: wavelength is the inverse of frequency.) If we take the longer-wavelength boundary of long-wavelength IR to be the upper bound of "DC to daylight", this means that the pulse has frequency components ranging from basically 0 to 20 THz.
In order to induce a voltage in an antenna (whether intentionally designed as an antenna or not), the antenna must be a reasonable fraction of a wavelength. If the antenna is too short, the EM field simply doesn't have time to sufficiently interact with the conductor to induce a voltage.
Even at 20 THz, 100 nm represents 1/150 of a wavelength, which is pretty far below what you'd expect to need for a reasonably efficient antenna, which at least for much lower frequencies you might begin to see somewhere around ten times that size (in terms of wavelengths).
Let's also rule out a direct EMP strike. (Let's face it, if someone hits your device with what is basically a lightning strike at point blank range, few things will survive unscathed.)
Given all this, would nanotechnology likely be affected by an EMP? Why or why not? What factors would contribute to susceptibility or non-susceptibility to EMP damage in a nanotechnology scale device?
I'm not tagging this hard-science, but the harder the science in answers, the better.