Those physical limits are surely though at a much finer resolution that common high end digital cameras?
I understand that you are saying that you see the effects even if you are not a the "molecule" level as you say, but I would think that the hard theoretic limit of photons should be at a finer granularity than high end digital cameras.
With the exception that holographic film images the diffraction pattern produced by two interfering laser beams, so typical grain size there has to be on the order of tens of nanometers. It can certainly be done, just is pointless for normal film =)
Essentially, a film grain or a cell on a CCD sensor is like a “bin” that collects and counts photons. As you make the area of the bins smaller, there are fewer photons collected in a given image, and statistical fluctuations from sampling become more relevant. You get more “noise” in the final image.
See https://en.wikipedia.org/wiki/Shot_noise