The rules aren't clear. For really effective hiding of large objects, the appropriate skill is probably:
Craft: Carpentry
or maybe profession: carpenter
You'll want boxes with false bottoms, secret compartments hidden in your ship, or both.
Depending upon how you are smuggling the items, you might even not need skill checks at all. If you have all your sailors swallow plastic (yeah, I know--probably doesn't exist in fantasy, but there may be a substance that has the same utility) bags filled with small and durable contraband just before landfall and pick it out later, there's no need for a skill check. The only way that the enemy would locate it is if they start to suspect something and then they are either patient enough to wait for the evidence to emerge or good enough at heal to discern that the people swallowed something indigestible. Likewise, if the items are watertight boxes strapped to the hull of your ship, anyone who looks is going to see them, but it is likely no-one will look. In that case, the relevant skill is going to be whatever you use to figure out that no-one is looking when you swim down and unload the cargo.
But for big items that you want to hide without special preparations? I would probably go with opposed search rolls. There might be a penalty to the roll of the guy hiding his items if he doesn't have the proper tools (boxes with false bottoms, etc as discussed above) or a bonus if the items in question are really small. Combining those two might work like this. The guy searching the ship makes his search check. If he beats the hide check he finds the contraband. However, if it was hidden in a specially crafted container, he would also need to beat the seach DC to find the hidden compartment. Thus, it is possible that a search check would find an item that was, for instance, hidden in a barrel of pickled fish but would miss that same item if it was hidden beneath the false bottom of that barrel of pickled fish--provided that the false bottom was well constructed.