We present an updated catalog of low surface brightness (LSB) objects and ultra-diffuse galaxies (UDGs) in the Coma cluster using g- and r-band images obtained with Hyper Suprime-Cam (HSC). This study expands upon work done in Koda et al. 2015 and Yagi et al. 2016, which covered about half the area of the Coma cluster and found 854 extended LSB objects, 332 of which qualify as UDGs with effective radii > 1.5 kpc. The HSC observations covered the whole Coma cluster out to its virial radius (an area twice larger than the previous studies) and doubled the numbers of LSB objects and UDGs with mr < 26.5 mag, corresponding to stellar mass > 106 M⊙. The new UDGs show internal properties (e.g., Sersic index of ~1) consistent with those of the previous studies, and are distributed across the cluster, with a concentration around the cluster center. The whole cluster coverage clearly revealed an excess of their distribution toward the south-west direction from the cluster center, where a known substructure exists (the NGC4839 subgroup). This suggests that at least some of the UDGs would be associated with the subgroup and possibly the large scale filament connecting the Coma cluster to Abell 1367.