$K_L \to \pi \nu \nu $ is one of the attractive processes to test new physics beyond the Standard Model (SM). It is drawing attention, thanks to the effort of the KOTO collaboration. In this talk, we briefly study the $K_L$ decay and other relevant flavor violating processes in a class of type-II two Higgs doublet models with extra gauged $U(1)_H$ symmetry. We sort few examples where the source of missing energy in Kaon decays is given by either dark bosons or massive neutrinos. We focus on the setup where effects of the extra gauge boson and of pseudoscalar portals will emerge primarily at the electroweak penguin level of $\Delta F = 1,2$ processes. We show that J-PARC KOTO most stringent upper limit for the branching ratio of $K_L \to \pi \nu \nu $ leads to important bounds for leptophobic and multi-Higgs $SM \otimes U(1)_X$ theories, at or below the electroweak scale, comparable to the limits provided by hadron colliders.