I can think of a few ways to exploit (meaning take advantage of, not violate the game's integrity) holding cargo in a stored ship.
However, none of them are game breaking in any way, nor convey an advantage beyond contracting the time required for some things.
There's some cases where the ability to store and transfer cargo between stored and teh active ship would solve minor issues. One of my pet peeves is taking on a sizable delivery mission in my type 7, only to find that the target destination is a platform I can't land on.