Server Side encryption slightly slows down performance when reading data from S3, both in the reading of data during the execution of a query, and in scanning the files prior to the actual scheduling of work.

Amazon throttles reads and writes of S3-SSE data, which results in a significantly lower throughput than normal S3 IO requests. The default rate, 600 requests/minute, means that at most ten objects per second can be read or written using SSE-KMS per second — across an entire hadoop cluster (or indeed, the entire customer account). The default limits may be suitable during development — but in large scale production applications the limits may rapidly be reached. Contact Amazon to increase capacity.