We have fallen for an inaccurate formulation in physics. What has been called the amplitude of EM radiation is in fact the intensity of the radiation. The amplitude of EM radiation per definition has to do with the intensity of the light.
The intensity of a monochromatic radiation - all photons of the same wavelength - has to do with the number of photons through a given area in a given time.
Hans Bethe wrote a paper in 1944, "Theory of Diffraction by Small Holes," Phys. Rev. 66, 163. He describes how he envisages the interaction between radiation and hole:
"The method is based on the use of fictitious magnetic charges and currents in the diffracting hole which has the advantage of automatically satisfying the boundary conditions on the conducting screen. The charges and currents are adjusted so as to give the correct tangential magnetic, and normal electric, field in the hole."
Since EM radiation consists of photons (and always does, there is no other method of generating EM radiation than by emitting photons), we can talk about an effective cross-section. If the hole is too small, the electric and magnetic fields of the electrons at the surface of the hole absorb or reflect the photons. If the aperture is too large, only the photons that come close to the edge are deflected, while the photons in the middle of the beam leave the aperture unhindered.