Although the accelerators of ultra-high energy cosmic rays (UHECR) are still not identified, we have new hope to constrain their properties using a multi-messenger approach. Every astrophysical environment, where UHECR nuclei are accelerated and interact with the dense photon fields, will also emit neutrinos. This depends on several modeling aspects of the related photo-nuclear physics in the energy range of the Giant Dipole Resonance and the Quasi Deuteron processes, and also in a regime where the production of pions occurs, which eventually will decay into neutrinos. We have studied in detail the properties of nuclear disintegration rates and chains inside candidate accelerators and during the extragalactic propagation of UHECR. We find that over-simplified models of nuclear interactions, which are often used in UHECR propagation codes and source models, have noticeable impact on the theoretical description of the source and they can introduce a systematic bias to analyses based on statistical arguments. These additional uncertainties can be potentially resolved with accelerator measurements.