SOLDIERs were always supposed to have two pauldrons, the SOLDIER enemies you fight did, they were just lazy with Zack's design (or he was genuinely that unimportant, take your pick). I don't think Cloud destroyed his right shoulder at some point on a job and damaged his left ad enough that the only way he could repair it is with sticking another plate on it with gigantic bolts sticking out. But it did accomplish the look what he wanted it too: "Ex-SOLDIER, but SOLDIER nonetheless, don't **** with me." I assume that he just got used to the weight distribution by the time AC rolled around.