Ummm... since when do dupes not count against you in ARRL contests? This comes directly from the ARRL web site under "Contests" and the tab for "Disqualifications and Penalties".
"For each duplicate contact that is claimed for credit and each miscopied call sign that is removed from the log by HQ, three additional contacts will be deleted as a penalty. The penalty will not be considered part of the 2% disqualification criteria."
Further, there is this little tid-bit:
"An entry with more than two-percent duplicate contacts left in the log or an entry in which more than 2% "rubber clocking" (altering the actual time to increase the operating time so that it is greater than the allowable limit) is detected will be automatically disqualified. "
That seems like a pretty good reason not to submit logs with dupes in it. Here is a link to the page: http://www.arrl.org/contests/dq.html