depends on the model/brand. if it's not worth much or has no collector value, taking it out of the box makes no difference.
not all boxes are sealed. display type boxes like some autoarts, ignition model, etc. that are not "airtight" are fine to keep the model inside. but those that are in jewel boxes or styrofoam clamshells... those can be bad in the wrong type of storage conditions.
if you take good care of your models and they remain in as-new condition with it's original packaging intact and in original shape stored somewhere dry (ie. not in a damp storage unit), it will hold it's value or more.
cooler temps, no direct sunlight (or hot lights like halogens), and as much of a dust-free environment as possible are key.
this is how the hardcore collectors do it:
