If indirect detection searches are to be used to discriminate between dark matter particle models, it is crucial to understand the expected energy spectra of secondary particles such as neutrinos, charged antiparticles and gamma-rays emerging from dark matter annihilations in the local Universe. In this work we study the effect that both the choice of event generator and the polarisation of the final state particles can have on these predictions. For a variety of annihilation channels and dark matter masses, we compare yields obtained with Pythia8 and Herwig7 of all of the aforementioned secondary particle species. We investigate how polarised final states can change these results and do an extensive study of how the polarisation can impact the expected flux of neutrinos from dark matter annihilations in the centre of the Sun.