Was in a battle chasing down a ship and suddenly the sea graphic I'm in and next to changed to the land graphic and back as the wave level rose and fell ("Storm map") - No waves crashing or other indication of shallow water. Sub-surface and near surface hazards and their inherent warning signs should be a core feature ("Iceberg! Dead ahead!").
Should I be chased (pirate, enemy belligerant, etc) and I'm in a shallow draft vessel it would be nice to have the option to brave the shaols and sandbars daring my pursuer to follow and risk grounding or, even worse, tearing a big hole in their hull. Or if I in a ship larger and better gunned than my target they should have the option to brave the coral reefs in a bid to escape.
But we'll need some signs of shallow water added - Waves far off the beach, old mast sticking up out of the water, etc.
Along with navigation hazards we should also encounter weather extremes (a truly PvE encounter) that could cause ship damage or even lead to capsizing should we set the sails incorrectly, not sail into the wind and waves, avoid land masses and sub-surface hazards and the like. Trying to skirt a hurricane/cyclone/typhoon and messing up your navigation could get you sucked into a PvE weather encounter - A few minutes (5-15, more or less depending on crew specialists, location, etc) of sheer terror.
Rogue waves might be a bit too much but could be added as a way to greatly endanger a ship from time to time.
Success would award experience points which could be based, as only one example, on how many seconds one was in the encounter and subtracting shiip damage. Epicly fail and... well there's always another ship needing a captain somewhere. Risk/reward and all that.