Yes, you can upload files whose names contain special characters or hidden characters to Amazon S3 using the Drag Drop and Upload Files to Amazon S3 app.
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