Where are AMIs stored?
AMIs and snapshots are stored on S3 in the standard storage class. You cannot access this area of S3 directly, only via the service web interface or APIs. You pay S3 standard rates for this storage.
There's no easy way to tell how much storage these "hidden" sections of S3 take up. The best way I've found is on the monthly bill.
Update: in Nov 2021 AWS introduced the ability to "archive" snapshots which moves them to cheaper storage, similar to glacier. The download is they're not incremental / block based they're the full snapshot. Given EBS snapshots are block based and incremental archiving snapshots where there are multiple snapshots for a given volume may not give you the savings you expect. I use it for archiving snapshots of VMs I no longer need running and only have a single snapshot of.
References (good as at December 2016)
Snapshots in S3 (link).
You can back up the data on your EBS volumes to Amazon S3 by taking point-in-time snapshots.
AMIs in S3 (link).
Amazon EBS-backed AMIs launch faster than Amazon EC2 instance store-backed AMIs. When you launch an Amazon EC2 instance store-backed AMI, all the parts have to be retrieved from Amazon S3 before the instance is available. With an Amazon EBS-backed AMI, only the parts required to boot the instance need to be retrieved from the snapshot before the instance is available.
EBS Snapshot Storage.
Snapshots occur asynchronously; the point-in-time snapshot is created immediately, but the status of the snapshot is pending until the snapshot is complete (when all of the modified blocks have been transferred to Amazon S3)
Where is that AMI stored? It is stored as an EBS Snapshot. In fact, if you try to delete this Snapshot, you will not be able to. You will get an error: Failed to delete snapshot... the snapshot snap-xyz is currently in use by ami-123.
Is it on S3? No, as stated above, it is stored as EBS snapshot. And it makes a big difference because EBS snapshot of SSD is $0.05 per GB, whereas S3 is $0.023 per GB, which is about half.
Will making extra AMIs be added to the amount paid each month? Yes, because it will be based on another snapshot.
Placing a pic of AWS bill, which helps to contextualize all these microscopic numbers.
Excerpt of an actual AWS bill