I'd check the helm station wiring first because bilge pumps operate without solenoids. Both float switches and helm switches and lights carry the full power to operate the pumps. If somebody was careless, they could have cross-wired the helm wires and the same circuit that runs the bilge pump light at the helm could be supplying power to the other pump.
Since both float switches operate both pumps, there must already be power to the plus side of each float switch and then somewhere there is a crossover wire that's supplying power to both pumps. It's kind of like a 3 way light switch! If it's unintentional (like the helm is cross-wired) you may only need to set it back straight.
Here's the next test. If you turn the helm (and flybridge if you have it) starboard bilge pump switches to "off" and then go operate the float switch for the port bilge pump, what happens? If it still operates both pumps, and the starboard float switch does nothing at all, my guess is that the "pump operating" lights are cross-wired at the helm or bridge.
If your wires have the original Hatteras numbers and you have your wiring diagram, it'll make it easier, but if not and if the above test works, then turn all switches to "auto", turn off the main power circuits, disconnect one helm wire, mark where it goes, protect it from shorting, turn the power back on and lift one float switch. If they both still run, continue to do the same with more helm switch and helm light wires until you find one that stops the crossover pump from running. If you remove one that stops both pumps from running, reattach that wire where it was and go on to others.
Of course, if you put the wires back right, that still leaves them on the same circuit, but that's a separate issue.
Doug Shuman