The interpretation of helium ion microscopy (HIM) images of crystalline metal clusters requires microscopic understanding of the effects of He ion irradiation on the system, including energy deposition and associated heating, as well as channeling patterns. While channeling in bulk metals has been studied at length, there is no quantitative data for small clusters. We carry out molecular dynamics simulations to investigate the behavior of gold nanoparticles with diameters of 5-15 nm under 30 keV He ion irradiation. We show that impacts of the ions can give rise to substantial heating of the clusters through deposition of energy into electronic degrees of freedom, but it does not affect channeling, as clusters cool down between consecutive impact of the ions under typical imaging conditions. At the same time, high temperatures and small cluster sizes should give rise to fast annealing of defects so that the system remains crystalline. Our results show that ion-channeling occurs not only in the principal low-index, but also in the intermediate directions. The strengths of different channels are specified, and their correlations with sputtering-yield and damage production is discussed, along with size-dependence of these properties. The effects of planar defects, such as stacking faults on channeling were also investigated. Finally, we discuss the implications of our results for the analysis of HIM images of metal clusters.