We present a quantum optics theory, numerical calculations, and experiments on coupled quantum dots in semiconductor nanowire waveguides. We first present an analytical Green function theory to compute the emitted spectra of two coupled quantum dots, treated as point dipoles, fully accounting for retardation effects, and demonstrate the signatures of coherent and incoherent coupling through a pronounced splitting of the uncoupled quantum dot resonances and modified spectral broadening. In the weak excitation regime, the classical Green functions used in models are verified and justified through full 3D solutions of Maxwell equations for nanowire waveguides, specifically using finitedifference time-domain techniques, showing how both waveguide modes and near-field evanescent mode coupling is important. The theory exploits an ensemble-based quantum description, and and an intuitive eigenmode-expansion based Maxwell theory. We then demonstrate how the molecular resonances (in the presence of coupling) take on the form of bright and dark (or quasi-dark) resonances, and study how these depend on the excitation and detection conditions. To go beyond the weak excitation regime, we also introduce a quantum master equation approach to model the nonlinear spectra from an increasing incoherent pump field, which shows the role of the pump field on the oscillator strengths and broadening of the molecular resonances, with and without pure dephasing. Next, we present experimental photoluminescence spectra for spatially-separated quantum dot molecules (InAsP) in InP nanowires, which show clear signatures of pronounced splittings, though they also highlight additional mechanisms that are not accounted for in the dipole-dipole coupling model. Two different approaches are taken to control the spatial separation of the quantum dot molecules, and we discuss the advantages and disadvantages of each.