It continues to irritate me that when they built a bridge tunnel across the James River here in Hampton Roads, the State of Virginia named it the "Monitor-Merrimac Memorial Bridge Tunnel", ignoring the fact that at the time of the battle, the ship was no longer the USS Merrimac, but the CSS Virginia.
It seems it has always been called the Merrimac in the history books I've read as well. My opinion is since it was in the service of the Confederacy it should be called by it's rebel name.