I dont think its unreasonable to give an attck penalty to a more heavily armoured version of basically the same troop type. If a guy has the same weapon, but heavier armour and is less maneouverable it would be more difficult for him to land a blow, but clearly the heavier armoured guy is going to hold the line better, which is the way most people use spearmen.
I guess the morale value is for more balanced gameplay rather than realistic reasons.