In the Making Of Aja Classic Albums documentary when they play Black Cow and Aja (the song) you'll notice they just play back the final mix, not isolated bits of the multitrack. The $600 thing came from the liner notes to the remastered Aja, and are a tongue-in-cheek joke - their liner notes are always slightly dismissive of the quality of their own music and putting a value of $300 (per song) on those two songs was sort of a joking way of showing how much they care about them.
The thing with multitracks is that back then no one ever expected they'd need to go back to them, often they were just left at the studio where they were recorded or where the final master mix was done. Often when these studios went out of business or were sold, the tapes were just dumped as they are quite large in size; a 2" master tape in it's box is somewhere in the neighbourhood of 3" x 12" x 12", and you would have at least one of these for a 24 track mix, or 2 for a 48 track mix, and so on. Just to give you an idea of how many tapes might be lying around, in an article I read, Jeff Porcaro related that they cut Gaucho (the song) almost 80 times, each on a new tape, before they got a rhythm track that they were happy with. So you can imagine after taking a year to record a whole album how much tape might be lying around the studio. There was a recent interview with one of the guys from Rush where they said they can't find the multitracks for a bunch of their albums because they left them at Trident studios in London when they'd finished doing the stereo mixes, and when Trident went out of business they (presumably) threw away all the tapes. This kind of thing is more common than any record label would admit.
I also recall someone saying (possibly on the Steve Hoffman board) that there was someone at MCA records sometime back that was selling multitrack tapes to Japanese collectors with deep pockets, and that Steely Dan wasn't the only band with missing multitrack tapes, but I don't know if this story has any truth to it.