The magnetic properties of site-disordered Ni5Sn(O2BO3)2 ludwigite have carefully been studied using local probes and bulk experimental methods in temperatures down to 1.6 K and magnetic fields up to 9 T. Our results have clearly shown the role of the effect of order/disorder site occupancy in these complex compounds with spin moments S=1. Different from most ludwigites, site-disordered Ni5Sn(O2BO3)2 ludwigite has shown three magnetic transitions at 80, 50, and 5 K. Local probes (Sn119 Mössbauer and muon spin spectroscopy) have indicated a partial long-range magnetic order with onsets at 80 and 50 K with predominant ferromagnetic interactions at 80 K and antiferromagnetic ones at 50 K. At lower temperatures, a partial spin-glass-like freezing of the moments has been developed concomitantly with fraction of the moments ordered at higher temperatures, a spin-glass-like and long-range magnetic order coexist and a spontaneous exchange bias effect has been observed. Applied magnetic fields have gradually reduced magnetic frustration, leading to a magnetically ordered state of the complete structure at 51 K under 9 T. The absence of double-exchange interactions in order/disorder Ni5Sn(O2BO3)2 ludwigites shows how the magnetic interactions that compete as direct exchange and double exchange are modified by the site occupancy of nonmagnetic Sn ions. Features as a third magnetic transition, the appearance of spontaneous exchange bias, and the enhancement of the coercive field at low temperatures were not found in the site-ordered isomer compound.