Jamal,
From my experience there is no noticeable difference between the two. What is better when using compact caches is copying caches from one server to another, i.e. From your development system to your production system. As the cache is in bundles it is a lot quicker to copy than millions of small individual files.
Regards
Anthony
I had encountered performance issues while using Exploded cache storage format.
However Compact cache storage format will be better, when you are map caching in multiple machines and to copy the cache files from one machine to other.