Crafting duplicates is blocked
Someone asked on the forums what the point of crafting a duplicate card was, and the honest answer was: there wasn't one. You can only equip one copy of a given card, and breaking a spare back down returns just a fraction of the shards you spent, so crafting a card you already owned only wasted shards.
Now, if you already own a card, the Craft option for it is greyed out with a note explaining why. Crafting a card you are still missing works exactly as before, so you can still target the specific cards you need to finish your deck.
Thanks for the good question.