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Should I submit unique e-mail addresses, will it set off some flags or filters if a single e-mail address submits hundreds of sites?
No filters or flags whatsoever if the same email address makes hundreds, or even thousands of Guidelines compliant submissions. Honest and active contributors could even benefit from using the same email address: we can sometimes spot those few of them right from the email address provided, and 99% of the times it's a good title/description for a valuable site, submitted to the right category. Gets added faster, obviously.
Well, if you really have hundreds of sites to submit you may consider becoming an editor and contribute to the growth of the directory as an editor. Or, you can continue submitting from the public side after having taken due time to read and understand the ODP Guidelines.