I have never had stuff accidentally find its way onto ephemeral storage. The ephemeral storage is mounted at a specific location of /mnt. Everything else on the system (OS, binaries, application code and resources) is stored on an EBS volume.
You have to specifically put something into the /mnt folder if you want it to be stored on the ephemeral storage. Any other location is safe and will persist through halts and stops.
In practice the only thing you should ever use the /mnt folder is maybe a Nginx disk cache, or as an alternative /tmp or something like that. Basically if stuff you don't want to lose is finding its way onto the ephemeral storage then you are doing something wrong.
It depends on your users. We have some users that are not super well-versed in AWS and they just see a big disk and put data there, and someone has to come back and move it to an EBS volume to make sure it's safe. /mnt is also used as a staging area for large files and the intention is always to move them to permanent storage when done, but that sometimes doesn't happen. /mnt is usually, in the non-AWS world, where the bigger, more authoritative disks, like an NFS mount to the NAS, would be mounted, so it's counter-intuitive to tell users to treat /mnt like /tmp. Even if someone is using /mnt as a temporary store because they understand EBS v. ephemeral, if they shut down from within the instance, they don't see any warning about the doom of the ephemeral data, and it may be unclear that a shutdown/system halt is the same as a "stop" in the AWS console, and they could lose the data that they had in the staging area unexpectedly.
There are plenty of plausible situations where an AWS user can find themselves with important, even just temporarily important, data on ephemeral. Whether those are the result of "correct" usage or not, it's beyond the pale to just zap that data away and tell the customer tough titties as soon as a shutdown command is issued.
You have to specifically put something into the /mnt folder if you want it to be stored on the ephemeral storage. Any other location is safe and will persist through halts and stops.
In practice the only thing you should ever use the /mnt folder is maybe a Nginx disk cache, or as an alternative /tmp or something like that. Basically if stuff you don't want to lose is finding its way onto the ephemeral storage then you are doing something wrong.