Yeah, I don't know about S3, but years back I talked a fair bit with someone that did storage stuff for HPC, and one thing he talked about is building huge JBOD arrays where only a handful of disks per rack would be spun up, basically pushing what could be done with scsi extenders or such. It wouldn't surprise me if they're doing something like that with batch scheduling the drive activations over a minutes to hours window.
I think that's close to the truth. IIRC it's something like a massive cluster of machines that are effectively powered off 99% of the time with a careful sharding scheme where they're turned on and off in batches over a long period of time for periodic backup or restore of blobs.
it's amazing that Glacier is such a huge system with so many people working on it and it's still a public mystery how it works. I've not seen a single confirmation of how it works..