There is a difference between a deck that is defective (e.g. 2 Aces of spades) and a deck that has a number of cards boxed.
Even if cards are boxed, there is an equal probability of drawing any given card for your hand, and you proceeded in the hand on that basis. Although it is true that if a card that improves your hand later appears and is boxed, or is prematurely put on the board, etc., it may change the flow of the hand, that exposed card could have equally been a card that did not help your hand. According to random card theory, there is no unfairness here as the affected card will have an equal chance to be a winning or losing card for all players.
A defective deck on the other hand (e.g. two Aces of Spades) means that the player who has one of the Aces of Spades, or who needs to draw one of the Aces, had/has a greater chance of drawing it and therefore, the deal is not truly random.
A defective or "fouled" deck has a very specific definition in my view.. I like the Hilton's rule here: "missing, mutilated or marked cards, one one or more jokers when none are in use, do not constitute a defective deck...", and boxed cards are treated separately (as a scrap of paper).
With boxed cards, I see no reason why the hand should not be played through when there already has been substantial action. Nick's suggestion to clarify the language is well taken. However, as Tristan pointed out, I'm not sure if we even need this - Rule #31 specifically outlines the conditions for a misdeal, and any misdeal cannot be declared once there has been substantial action.
With respect to the one boxed/one exposed card by the dealer situation at the beginning of the hand, strictly by the book, there is no misdeal; but if no one has yet to act, I'd personally be tempted just to call it a misdeal to avoid the bad situation potentially snowballing especially if there are further boxed cards in the deck.
During the hand, (after substantial action has occurred), if my dealer finds a boxed card and lets me know, I'd also be tempted to check the rest of the deck before action continues to see if there are any other boxed cards, and if there is more than one additional boxed card (i.e. three or more in total), I'd be inclined to turn the boxed cards over and reshuffle, not much unlike a prematurely exposed flop. This is a bit unconventional, but I think it is fair and addresses the issue of a deck having a whole clump of boxed cards, and then having to expose them to all the players and expect them to continue with knowledge of those cards.