I don't think there are any effects (yet) that cause any of the item decks to be shuffled.
I can think of one exception.
Gabriel's ability is:
ANYWHERE: Once per round, when
Gabriel is at a location with a
search deck, you may reveal the
top 4 cards of that search deck.
If you revealed any outsider cards
you may place 1 into your hand.
Shuffle the remaining cards back
into the search deck.