Any time you add excludes you create more overhead for the mechanism providing 
the stream of data to the backup application.  More than likely traversing the 
file system will be slower than if the files/stubs didn't exist, but the 
aggregate throughput will likely increase by not having to move as much data 
across your network.  It depends on how much of the total amount of data is 
being archived, how many files that is, the read speed of the file system and 
the link speed of the network.

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