- Yes, the files are uploaded with versioning.
- If the same-named files are uploaded, then a version suffix will be added to each file name in a numbering sequence (e.g., v1, v2, v3....)

PS: View Drag, Drop & Upload Files to Amazon S3, a Salesforce AppExchange app for moving files from Salesforce to Amazon S3: https://appexchange.salesforce.com/appxListingDetail?listingId=a0N3000000B5ZPqEAN