We rented a car from Hertz right in Warnemuende last August, reserved by phone to the Rostock location. The Hertz office is to the right of the dock in walking distance. We also had trouble getting any info from Hertz in the U.S., finally called Hertz in Rostock (they speak English) and reserved the car. Tell them you're coming into Warnemuende. I believe the number is 001-49-7699653. They did not have e-mail.
We had a great day driving to several nearby cities via the nearby autobahn. Gasoline was very expensive. Our ship stayed overnight, so we didn't have to worry about returning early. Warnemuende itself is a cute town to walk around.