Something we happen to agree on.
Except that the other Spherus Magnans would also have no reason to suspect it, leaving the Makuta just as vulnerable as everyone else.
Granted, if some were using their Stasis Field power at the time, they might survive it's activation, since it also renders them damage immunity.
But again, if they don't know what's happening, they wouldn't know to use it.
The GSR's Gravity powers alone could probably be used to toss it into a black hole or something equally ridiculous, provided it had enough prep time.
A well-known and feared device from one galaxy could resemble a paperweight in the eyes of those from another. And, due to the distance, the HF and Bionicle sides are likely completely in the dark regarding each others' existence. If someone discovered Atlantis, for example, told no one of its location, and then proceeded to blow it up and destroy all evidence hinting at said location, no one would ever be the wiser. Same with the Doom Box itself; if it's current whereabouts are unknown to the populace at large and they were also unaware of its usage, no one aside from Core Hunter would know where to retrieve it from.
Granted, I'll admit that if merely holding the device granted immunity from its destructive properties, then that's another situation entirely. But in order for that to be confirmed or not, we'd need to run that by Greg.