The Janitor is the system by which unused items are deleted from the game.
Items on the ground are considered unused. Do not leave anything on the ground, in or on other objects, or anywhere but on your character or in a locker if you are serious about keeping the item. This includes items that are meant to be placed on the ground, like alchemy cauldrons and racing roltons.
Some things are taken in less than a second. Other things hang around for hours. Don't take the chance.
The janitor will not clean a room if a player is present. There is a haze/whirlwind event that will clean up a room if a player is present, but it first gives them a 20 second warning:
A gray haze hovers for a moment.
A small whirlwind races past the area.
After the warning, it will return with:
A gray haze covers the ground for a moment.
A small whirlwind races through the area.
This event is only present in specific areas, usually hunting grounds, so bashing your boxes in/around town shouldn't be an issue.
In most cases, if you're losing boxes to the haze/whirlwind, it's because you're choosing to open them in such an environment to offset a game mechanics penalty (usually encumbrance). That's fine, but it's you who are making the decision and accepting the risk.