Regarding the ship modifications found in the S&S player's guide: Would you consider it legal to stack "Sturdy Hull" with "Wooden Plating" or "Armor Plating", or is this illegal for the same reason that worn armor and mage armor cannot stack?
Pr. the rules, neither type of hardness increase is a named bonus. And since unnamed bonusses stack, I'd allow it.
That being said, it doesn't really matter. Ship-to-ship combat in S&S is irrelevant. A ship has 1620 hp! Having a hardness of 5 or 11 won't do any difference. The main thing about ships is sailing modifier, and thus armor plating is a very poor choice.
I think the fact that a ship's HP is so high, compared with the damage that siege weapons do, actually makes hardness important -- suppose it takes 40 hits to sink a ship normally with siege weapons, but hardness is taking away an additional 6 damage from each hit -- that means it takes another 10 or so hits to do it in -- in a battle where the goal is sinking ships, that can make a big difference.
Now, granted, most of the time players in S&S won't want to sink the opposing ship. They'll want to use the siege weapons to damage them a bit, maybe take out some of the crew, and then close for boarding. And if the ship appears to be too strong to take, they'll want to GTFO ASAP. So, yes, armor makes little sense for the player's pirate ship.
As a GM, I would allow sturdy hull to stack, but not the 2 types of plating. It seems to me this would follow the "types of bonuses" default rule. Also - look at things that reduce/increase cargo space this way for mutually exclusive items... I don't allow my players to have things like narrow hull and expanded hold stack.