A Storm Giant’s AC is 16 due it its scale mail, and it has a Dex modifier of +2, so without the scale armour the giant’s AC would be 12. However, a Cloud Giant has a Natural Armour of 14 and a Dex modifier of +0, meaning its AC calculation is [10+0+Y], where +Y is its natural armour bonus (thick/magical skin), in this case +4.

Does this mean the more powerful Storm Giant does not have this natural armor bonus? If its scale mail is taken away, would its AC be 12, 16, or something in between?

Hill Giants have a Dex modifier of -1 and a Natural Armour of 13, indicating their natural armour bonus (+Y) is also +4.