If I understand your question correctly:

Loot crates are found after broadside-only combat.
Treasure chests are found after hand-to-hand combat.

Johnny Ringo on Oct 11, 2012 wrote:

there are also "secret chests" hidden throughout the game. Keep an eye out!

Quick question about these secret chests. Are they in the same spot for everyone and gettable once or are they like Wizard101 chests and respawn from time to time?

wander free on Oct 10, 2012 wrote:

Hi,
Are the treasure chests and the loot crates the same thing? After battle I quickly pick up the treasure chests but have never found a loot crate. What does it look like and where can I find it? Am I missing something here?

After the hand -to-hand battles you will find the treasure chests. The ones you have already been running around to pick up.

In the broad side battles (ship-to-ship), when you sink a ship it leaves debris in the sky. That debris is the crate of loot to pick up after the battle. Just like you have to run around to get the treasure chests, you also have to sail out to the crates to pick them up. I know there are areas with wreckage floating around in the sky, that is not what you pick up (other than if a quest asks for it), so don't let that confuse you. Only the debris left after the broadside battle is the loot in the crates you are looking for.

I hope that helped you a little.