In the 2004 Bionicle comics, the Toa try to hide from the Vahki by stowing away on an airship. Unfortunately for them, a group of Nuurakh are already there, ready to attack. Matau wasn’t expecting this, which means that the Vahki don’t normally guard airship cargo holds. During the fight with the Vahki and then Nidhiki and Krekka, many of the cargo boxes were damaged.
Now maybe the Vahki just thought the Toa Metru might escape this way. But let’s have some fun and say what if that cargo was the most important thing in all of Metru Nui, and the Toa destroyed it.
I’ll start: maybe it was proof that Teridax had replaced Turaga Dume.
I haven’t read the comics but if I had to guess (assuming the cargo’s important) I’d assume either upgrades for the Vahki that would make them tougher or smarter or important armor/Kanohi for an army Teridax could have been building (or Rahkshi parts?).
The simple, most likely answer is that the crate had security because it was full of valuable artifacts or precious metals.
The most interesting “what if” scenario I can come up with, though, is that the crate was part of a plan to prevent Teridax’s interference in Metru Nui. What if some underground “rebel” group had pieced together that something was wrong with Turaga Dume, and that crate contained something that would have stopped Teridax’s scheme, or at least part of it?
Now, I’m not saying that they would have stopped the whole Plan, or even the Great Cataclysm; I doubt that that much of Teridax’s plan could have been figured out and unraveled by a handful of Matoran “criminals”. More realistically, though, someone might have figured out that the Matoran Spheres were bad news and was going to put a stop to them with the contents of that crate.
I stand by my prior answer, it was perfect and will be forever, but a potential alternative in a worse world could be the answer Tahtorak was looking for