Yes and that's why investing in super heroes sets is a risky game if you're not aware of the news, because once an exclusive minifig can be found in an other set, boom, the first set does not sell anymore.
The only exception is when the "old" minifig is a bit different (I'm thinking about wolverine right now), so hardcore collectors would want each version of wolverine. But you have to be lucky to sell it to this kind of collector.
Most of the kid will just be happy with the new version, even if the belt on the minifig is not exactly the same...
But as you said, when the potential of the set is also based on vehicles, that's not the same scenario: might the minifigs be no more exclusives, people can still be attracted by the vehicule/building.
You're talking about the AA: even if minifigs all appear one day in other sets, there would still be the mansion (it's far more than just a bonus !) which does have real value : http://www.ebay.fr/itm/LEGO-DC-Universe-Super-Heroes-Batman-Arkham-Asylum-Breakout-10937-NO-MINIFIGS-/261712941783?pt=Building_Toys_US&hash=item3cef4e92d7
(55% value of the whole set compared to new items)
On the other side, put apart minifigs of the 6866 Wolverine's Chopper Showdown and you'll just see a "meh" helicopter... Listings on ebay show that this helicopter is worthless (well, the price of the bricks: http://www.ebay.fr/itm/Lego-Marvel-Deadpools-Helicopter-Only-from-6866-No-Minifig-No-Box-No-Bike-NEW-/400654374008?pt=Building_Toys_US&hash=item5d48dc9478 )
(25% of the value of the whole set compared to new items)
(these examples might not be the best ones but they give an idea of what I mean)