The design and the characterization of functionalized gold nanoparticles supracrystals require atomically resolved information on both the metallic core and the external organic ligand shell. At present, there is no known approach to characterize simultaneously the static local order of the ligands and of the nanoparticles, nor their dynamical evolution. In this work, we apply femtosecond small-angle electron diffraction combined with angular cross-correlation analysis, to retrieve the local arrangement from nanometer to interatomic scales in glassy aggregates. With this technique we study a two-dimensional distribution of functionalized gold nanoparticles deposited on amorphous carbon. We show that the dodecanethiol ligand chains, coating the gold cores, order in a preferential orientation on the nanoparticle surface and throughout the supracrystal. Furthermore, we retrieve the dynamics of the supracrystal upon excitation with light and show that the positional disorder is induced by light pulses, while its overall homogeneity is surprisingly found to transiently increase. This new technique will enable the systematic investigation of the static and dynamical structural properties of nanoassembled materials containing light elements, relevant for several applications including signal processing and biology.