Crates represent item pick-ups floating in the water.
Small money crate is usually dropped by a defeated boat. It represents small amount of money that was on the dead boat. Any boat can pick up this item.
Big money crate is payment for safe return of captured commercial ships. Since these crates are bigger then usual, only correctly equipped boats can pick them up.
Health create can be found randomly floating in the water or it can be dropped by a defeated boat. By picking up this crate, boats can get repairs done in the middle of the battle. Any unused value of the crate is converted to money.
Special weapons crate contains up to two special weapon items. Like health crates these can be left by defeated boats, or be found in random locations.
Next three crate types are very rare and can only be occasionally found in random locations on map.