On mine, the top card tends to be around 5 or 6C hotter than the bottom. But this isn't really the important issue; the cards are designed to operate within a fairly wide thermal envelope (up to 95C), so what you really care about is fan speed. On mine, the top card can use up to 10% higher fan speed. Typically I will find the top card using around 70-75% fan speed when under full load in games, with the bottom card on 60-65%. In furmark the top card can get up to 90% fan speed, but I never see anywhere near this in games.
The "obstructed" top card does not suffer quite as badly as you might think, since the primary source of cool air is from the back end of the card (which is not obstructed). The fan still creates a pressure drop roughly equivalent to an unobstructed card, so airflow is not significantly affected. What you lose out on is airflow over the exposed metal on the top of the card, but as a cooling mechanism this is secondary to the air intake and heatpipes.
I should point out, that I'm also using a HAF-x with a very slow 120mm fan in the intake duct (similar to redgooner's picture), so I feed cool air directly into the cards. In a less well ventilated case, expect to see an extra few percent of fan-speed.