Highly uniform arrays of site-controlled GaN nanowires are synthesized by selective area growth using a Si3N4 mask and molecular beam epitaxy. Systematic modulation of the emission along the nanowire axis is observed in spectrally resolved cathodoluminescence linescans. We show that this intensity change is an indicator of unintentional Si incorporation during growth resulting from the interaction between the impinging Ga atoms and the mask material. The gradual reduction of the cathodoluminescence intensity along the nanowire highlights the important role of the growth geometry within the synthesis reactor, with shadowing from the elongating nanowires inhibiting the reaction with the mask. This gradient in Si doping is confirmed by the quenching of the longitudinal optical phonon line measured in Raman spectra along the nanowire axis. The corresponding carrier density is derived from the frequency of the coupled phonon–plasmon mode. The spectroscopic identification of inversion domain boundaries in the majority of the nanowires is also attributed to the Si incorporation. From temperature dependent cathodoluminescence experiments, we derive the activation energy for excitons bound to these defects.