Both phrases can be used to mean "never was" or "was but it has been undone".
For example, if I say "The order is not boxed", I probably mean that it never was in a box. But I could mean that it was in a box and then someone took it out of the box. (Perhaps because it was the wrong kind of box, or they needed to inspect the item, or whatever. Reason is beside the point.)
Likewise, if I say, "The order is unboxed", the same two possibilities exist.
Same with "not loaded" and "unloaded". In the real world one of the interpretations may be unlikely. Like if I say, "The gun is not loaded/unloaded", maybe it's a brand new gun that was never loaded, but more likely the ammo has all been fired or removed. But if I say, "The order is not shipped", it probably has never been shipped. It's possible that it was shipped and then returned and needs to be reshipped, but probably not.
Note that "unloaded", or "un-" most anything, as a verb, means the process of undoing. If I say, "I am unloading the gun", I mean there was ammo in it and I am removing it. Because it wouldn't make sense to say that I am unloading it if it never was loaded.
If you want to make clear whether you mean "never was" versus "was but now isn't", you have to use additional words. Like, "This order was never boxed", versus "This order was boxed but has now been unboxed."