I've found the boards with skulls on them at the base of the Pirate's Stronghold.
As I recall from the N64 version, you have to remove those boards to enter the stronghold as the Iron main gates never open.
However, none of my attacks or items usable as Zora Link seem to affect those boards.
How do you remove those boards?
Best Answer
As you must have noticed, Zora Link's controls have been changed from the original in the 3DS version.
One of the changes you probably haven't noticed is that, while he normally swims slower than in the original, he uses the higher speed while the magic barrier is on.
In other words, you can make him swim fast by holding down R. This will break the boards.
Alternatively (this worked in the original too) you can walk on the ocean floor and roll by pressing forward and A while holding down L, to break the boards like normal Link would if they were on the ground.