There is a considerable interest for producing and understanding the optical and spectroscopic properties of ordered nanoparticles assemblies. Herein, we describe and interpret the optical absorbance and Raman properties of silver 5.9  0.3 nm diameter nanocrystals coated with dodecanethiol organized in highly ordered 3D superlattices of different heights. Each superlattice could be studied individually. A model based on Maxwell-Garnett formulation reproduces qualitatively the height and wavelength dependence of the absorbance. Importantly, because of their small size compared to traditional nanoparticles used in SERS, the large 3D distribution of hot spots generated by the silver superlattices allows to obtain easily SERS spectra of the surrounding ligands despite their intrinsic low Raman cross section. Accordingly, traces of thiophenol can be very easily detected.