Well, I don't think too many dead bodies are left in the planes in a legitimate airplane graveyard, but you never know.

The players won't be asking questions until they've finished killing/running for their lives.
The graveyard could be home to a growing toxyderm about to go on a rampage.
The vintage WWII planes might be disappearing because aliens, whose probes (foo fighters) witnessed these flying machines during the war are collecting them; Maybe for an alien museum, a collection of human artifacts telling the story of our existence.
Maybe creatures that end up in the graveyard have started to come back out horribly mutated. One of the planes contains a Nazi super-weapon that was captured by an allied war hero. The weapon was forgotten about or never discovered by the government at large and its strange properties/energies are twisting whatever gets near it.
The spirits of countless plane crash victims haunt the aviation graveyard and they are becoming increasingly restless. The spirits have begun to merge with the scrap creating gear golems, and things of that nature. Three words, Animated Jumbo Jet.
In that same vein; the fallen heroes of the war (whichever war that may be) cannot rest and their planes rise aloft at night with an eerie glow. These Flying Dutchmen of the air patrol the nighttime sky seeking out their enemies. Perhaps somewhere there is a scrapyard full of enemy planes undergoing the same supernatural phenomenon...
The enemy planes need to be destroyed before the innocent populace comes to harm during one of these twilight raids. Then the heroes of yore can finally rest.
Edit: Something is hidden in the graveyard that a number of organizations with evil aims want. Maybe it's hidden technology from the war, maybe it's the remains of a UFO that collided with an aircraft, who knows. Whatever IT is, the PCs must retrieve it and make sure that it never falls into the wrong hands.