Atmospheric pressure metal-organic chemical vapor deposition was used to synthesize Ag-containing ZnO nanostructures of different morphology on Si substrates coated by Ag. Ag from Ag/Si substrates and Ag from silver acetylacetonate after its decomposition were used as a catalyst for ZnO nanocrystal growth for deposition of ZnO nanostructures with different morphologies. We investigated the relation of the structural parameters and chemical composition probed by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and Raman spectroscopy with the photoluminescence (PL) properties and electron-phonon coupling (EPC) reflected in the multi-phonon Raman spectra. The Raman and PL spectra were studied at different powers of the exciting laser radiation (Pexc). The spectral position and width of the phonon Raman peaks and the near bandgap PL (NBPL) band at low Pexc are supposed to be determined by the structural quality of the surfaces/boundaries of the crystallites. The intensity of the near-bandgap and defect-related PL and the magnitude of the EPC are additionally affected by the dopant concentration. Because of the large crystallite size (>30 nm, determined from XRD), the effects of phonon or electron confinement are negligible in these nanostructures. The behaviour of the position and width of phonon and PL bands with increasing Pexc indicates that the heat dissipation in the film, which is dependent on the nanostructure morphology and Ag content, plays an important role. In addition, the cytotoxicity of ZnO:Ag nanostructures was investigated by using monolayer cell cultures of epithelioid origin MDBK (Madin-Darby bovine kidney) and MDCK (Madin-Darby canine kidney) cells at a MTT assay revealing that the level of silver doping of ZnO nanostructures, their morphology, and geometric dimensions determine their toxic effects.