  We prove an equidistribution theorem for a family of holomorphic Siegel cusp
forms for $GSp_4/\mathbb{Q}$ in various aspects. A main tool is Arthur's
invariant trace formula. While Shin and Shin-Templier used Euler-Poincar\'e
functions at infinity in the formula, we use a pseudo-coefficient of a
holomorphic discrete series to extract holomorphic Siegel cusp forms. Then the
non-semisimple contributions arise from the geometric side, and this provides
new second main terms $A, B_1$ in the main theorem which have not been studied
and a mysterious second term $B_2$ also appears in the second main term coming
from the semisimple elements. Furthermore our explicit study enables us to
treat more general aspects in the weight. We also give several applications
including the vertical Sato-Tate theorem, the unboundedness of Hecke fields and
low-lying zeros for degree 4 spinor $L$-functions and degree 5 standard
$L$-functions of holomorphic Siegel cusp forms.
