It seems like you are mixing light flux (given in lumens) with illuminance (given in lux, which is lumens/m^2). Anyway, you don't count the photons. Basically you are measuring how much energy is transfered from the source to the detector in the unit of time. If source varies with time faster then detector can detect it, you will get average result.
Photons are bosons, and they can occupy same quantum state, according to the Pauli exclusion principle. That means that they are free to move 'through each other' without colliding. If that were not the case our world would look a lot different.
Anyway when speaking about light duallity, and when considering photons as particles it is wrong to picture them as little blobs of matter, because they are not that. Photons are smallest possible 'packages of energy'.