I think they do.
NPC's placed via toolset, fire their onSpawn script as soon as the server starts up/the area is loaded, in which case the area will register them as being 'in' the area.
Quick way to test it would be to add this to the onArea enter script
void main()
{
object oEnterer = GetEnteringObject();
WriteTimeStampedLogEntry(GetName(oEnterer)+" entered the area");
}
Fire up your module, and see if the log contains the name of the npc's in the area.
Note - when we say onEnter script, it is the 'area' on enter, I dont think NPC's could fire a Module onClientEnter, because they are not Clients.