I was in the game with jimbob, here's what we found (or didn't find for that matter)
This only applies to the smaller wooden crates, not the large red or gray metal ones.
The small cube boxes are highly destructable. We used knife, any gun, and grenades to destroy them.
It only seemed to make the zombies stronger, but could not verify because we were in the teens when we found we could destroy them (found them going back to get someone jugger).
There seems to only be 4 that we have found.
The 2 I remember the locations of are on the back half of the ship (all are that we have found):
1. Immediately right of the steps down from the zip line, part of the semi-circle around the hole in the side of the ship.
2. To the left of the zipline stairs heading towards the mystery box location. There is 1 small crate on top of 2 larger rectangular wood crates.
The larger rectangular boxes seem indestructable. We shot, knifed, grenaded, crossbowed and used the scavenger on/near them. Nothing happened.