Thanks for using this forum to ask questions. We on the Cloud ONTAP Team appreciate it.
Yes, you would still pay money for those EBS snapshots of boot and root volumes. I am not sure if this is by design or not -- that by deleting the WE the snapshots are left behind -- but I have talked this through with the team and we feel this would be a great enhancement to Cloud ONTAP/OCCM. As a result, I have opened an enhancement request against a future release. Unfortunately it is likely much too late to get this into R1.0.1 or perhaps even 1.1, but I will make sure it gets attention.
Thanks again, and please do not hesitate if you have any further questions, even if unrelated.