Concrete, bone and shale have one thing in common: their load-bearing mineral phase is a hydrated nanocomposite. Yet the link between material genesis, microstructure, and mechanical performance for these materials is still an enigma that has deceived many decoding attempts. In this article, we advance statistical indentation analysis techniques that make it possible to assess, in situ, the nanomechanical properties, packing density distributions, and morphology of hydrated nanocomposites. These techniques are applied to identify intrinsic and structural sources of anisotropy of hydrated nanoparticles: calcium-silicate-hydrate (C-S-H), apatite, and clay. It is shown that C-S-H and apatite, the binding phase in, respectively, cement-based materials and bone, are intrinsically isotropic; this is most probably due to a random precipitation and growth process of particles in calcium oversaturated pore solutions, which can also explain the nonnegligible internanoparticle friction. In contrast, the load-bearing clay phase in shale, the sealing formation of most hydrocarbon reservoirs, is found to be intrinsically anisotropic and frictionless. This is indicative of a 'smooth' deposition and compaction history, which, in contrast to mineral growth in confined spaces, minimizes nanoparticle interlocking. In all cases, the nanomechanical behavior is governed by packing density distributions of elementary particles delimitating macroscopic diversity.