Even if it wasn't standerd practice in any of the other Vaults I'm sure Vault 101's Overseer (Bastard) would not let those bodies go to waste. Just look at the way he treated Amata.
I doubt the remains would go to waste in any of the vaults. It's a resource, and in the vault every resource would have to be renewable somehow.
Well, Vault 15, 8, 12, and other vaults that opened early, or after the planned 10 years might be the exception. Realistically though, for a vault to operate successfully, it would have to be completely self contained, and that means recycling/reusing of EVERYTHING.