Yes. I don't tend to use it anymore, so it's easier to play with 1 less card than keep cycling it round in my hand.
Taking it out of the deck effects gameplay. You can never move the second card to the back of the deck so leaving it out gives you better options. You may have been forced to move the front card to the back if the large market showed up and you had no actions available for either. Lets say because you left it out a free resource action was there in its place...this would give you the option to cycle the second card and possibly get a resource that allows you to use your first card forgoing the forced action of moving it to the back and essentially missing a round of upgrade for that card. Hope this makes sense to you I suck at explaining my thoughts.