We determine the irreducible components of Igusa varieties for Shimura varieties of Hodge type and use that to determine the irreducible components of central leaves. In particular, we show that the discrete Hecke-orbit conjecture is false in general. Our method combines recent work of DAddezio on monodromy of compatible local systems with a generalisation of a method of Hida, using the Honda-Tate theory for Shimura varieties of Hodge type developed by Kisin-Madapusi Pera-Shin. We also determine the irreducible components of Newton strata in Shimura varieties of Hodge type by combining our results with recent work of Zhou-Zhu.