Assuming you're talking about wet-cell batteries (not Optima or other AGMs), two 6 volt batteries are better than two 12 volt batteries.
Golf cart batteries are true deep cycle batteries - they're made for long, deep discharge cycles. Due to economies of scale (they have a huge market in electric golf carts) they're pretty much the best bang for the buck. Too often 12 volt "RV/marine" deep cycle batteries are a compromise between deep cycle and starting uses, not really best for either use.
The dual 6-volt version has half as many cells, so for a given total amp-hour capacity, each cell will be twice as large as the cells in the 12 volt version. Bigger is better in deep cycle usage - larger plates, more electrolyte, etc.
The 6 volt batteries will be connected in series, meaning there's one and and only one current path through them. All of the cells are charged and discharged at equal rates, keeping them in balance with each other.
A pair of 12 volt batteries connected in parallel divide the current between the two batteries. Under ideal circumstances, each battery will get half of the total charging current and will contribute half of the load current. But things are frequently less than ideal. A little bit of terminal corrosion, unequal amounts of wire resistance or changes in the battery's internal resistance frequently make one battery work harder than it's mate, decreasing the overall performance of the pair.
6 volt batteries are slightly taller than their 12 volt counterparts - make sure you have enough vertical clearance for them.