If a unit is enablesimulation false && hideobject true and is outside vehicle, they are hidden and do not simulate as expected. The moment they are moved into cargo they are unhidden and begin simulation again. This is true even if you run enablesimulation && hideobject again when units are in vehicle, they simply will not halt simulation or hide (up to and including shooting from vehicle).
Tested commands that do not work on units mounted in vehicles (MH-9 Hummingbird tested in this case):
_x disableAI "TARGET"; _x disableAI "AUTOTARGET"; _x disableAI "MOVE"; _x disableAI "ANIM"; _x disableAI "FSM"; _x enableSimulation false; _x allowDamage false; _x hideobject true;