The letter change on the URI scheme makes a big difference because it causes different software to be used to interface to S3. Somewhat like the difference between http and https - it's only a one-letter change, but it triggers a big difference in behavior.
The difference between s3 and s3n/s3a is that s3 is a block-based overlay on top of Amazon S3, while s3n/s3a are not (they are object-based).
The difference between s3n and s3a is that s3n supports objects up to 5GB in size, while s3a supports objects up to 5TB and has higher performance (both are because it uses multi-part upload). s3a is the successor to s3n.
If you're here because you want to understand which S3 file system you should use with Amazon EMR, then read this article from Amazon (only available on wayback machine). The net is: use s3:// because s3:// and s3n:// are functionally interchangeable in the context of EMR, while s3a:// is not compatible with EMR.
For additional advice, read Work with Storage and File Systems.
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