This paper is an extension of Kim et al. (2020a), and we prove equidistribution theorems for families of holomorphic Siegel cusp forms of general degree in the level aspect. Our main contribution is to estimate unipotent contributions for general degree in the geometric side of Arthur's invariant trace formula in terms of Shintani zeta functions in a uniform way. Several applications, including the vertical Sato-Tate theorem and low-lying zeros for standard L-functions of holomorphic Siegel cusp forms, are discussed. We also show that the "nongenuine forms", which come from nontrivial endoscopic contributions by Langlands functoriality classified by Arthur, are negligible.