All the time. Probably the most famous is the SS Great Eastern which was a cable layer.

You have to understand that paddle wheelers come in two main types. The first are like the Great Eastern, they have a large paddle wheel on each side. Typically they are traditional deep ocean hulls with the simple addition of steam power. Sometimes they appear as the inshore and river craft such as the Maple Leaf with broad superstructures placed atop a surprisingly traditional hull. The Eureka is a ferry of this type which you can visit in San Franciso. She was used for moving cars across the bay. The Eppleton Hall, just across the dock, is a very small example of the first type. She is not available for touring and is scheduled for major overhauls, so she may not be at the museum right now. I'm not sure.

The other type, and what I think you may be thinking of, is the aft mounted paddle wheel ship. This photo of the Bluff City is an example of this type. These were customarily river vessels with a very shallow draft. They were made for sailing on calm river waters and were not suitable for open water. They could be almost flat on the bottom and move through the shallows, which while valuable on a river or large creek, would make the ship impossible to control on the ocean.

The other main methods of propulsion at the time paddle wheels were common was sail and screw propellers.

One of the more unusual designs attempted was the ill-fated Hunter Wheel This was a sideways mounted underwater paddle wheel. Performance was poor and the idea was shelved.