I have to question the numbers that all this is based on.
Example: As a consumer, I can buy a 60GB drive for $45 (newegg.com). I'm thinking Apple can get a better deal than $37.50 for a 40GB HD. Or is iSuppli saying that Apple doesn't even get a 20% discount from the consumer price for an oem drive ordered in the tens of thousands? Come on. That doesn't add up.
Is Apple taking a lower margin -- could be, but I'm not going to base that conclusion on iSuppli numbers, which don't seem very reliable. Even if they are taking lower margins, I doubt they are as low as iSuppli's numbers claim.
My general understanding of hard drives is smaller capacity drives are more expensive. There is so much one can do to reduce the cost of such a small drive. After a while it is more cost effective to just increase the drive size (capacity).