It is important that the host can sustain the initial hit. This technology requires memory and CPU processing to perform the data deduplication. It might be a good idea to run the initial backup over a weekend when the backup window is a bit longer.
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Some companies are taking steps to mitigate this initial performance hit. I recently talked to Symantec, and, for that initial backup, they are putting some of the intelligence out on the individual nodes so there is some level of deduplication taking place before it takes off to help reduce some of the overhead.
Check out the entire Data Deduplication FAQ.