If your the AHJ, you would have to decide how likely it would be for this pipe to become energized. If so it would require a bond wire to be run to the pipe, and then bond the two pipes together.
Is the copper pipe from the cold water service? Does the copper pipe go elsewhere where there may be an electrical device with an equipment grounding conductor that bonds the pipe?
Sounds like the copper would be stubs of pipe coming off the water heater to attach the house plumbing to. I see no reason to bond such small peices of pipe.