6 - 6volt batteries is a lot more than 2 - 12volt batteries (depending on specific models likely more than 3 times as much). Of course, it will cost and weigh a lot more also.
Assuming you meant 2 - 6volt vs 2 - 12volt, I would lean toward the 6volt option. 6volt golf cart batteries are true deep cycle batteries. Most dual purpose 12volt batteries really are built as starting batteries and get a different label. If you draw them down deep, they won't hold up as well as a true deep cycle battery.
The amperage draw from the 5er will be low enough that either can handle the draw. The 6volt option will likely hold more amp-hours and hold up to being drawn down better in the long term.