We analyze $pA$ interactions at ultra-high energies within the semiclassical approximation for high energy processes accounting for the diffractive processes and a rapid increase with the incident energy of the coherence length. The fluctuations of t
he strength of interaction expected in QCD and momentum conservation are taken into account also. We evaluate the number of wounded nucleons in soft and hard processes, the multiplicity of jets in the proton fragmentation region as a function of the variance of the distribution over the interaction strengths directly measured in forward diffractive $pN$ scattering for RHIC and LHC energies. We argue that these results could be used to test whether parton configurations containing a parton carrying the $xge 0.5$ fraction of the projectile momentum interact significantly weaker than on average. We also study leading twist shadowing and the EMC effect for superdense nuclear matter configurations probed in the events with larger than average number of wounded nucleons.
