It seems the best bet is to go with the multiple 6V batteries as I'm more likely to get true deep cycle behavior I need from the batteries.
If the materials were guaranteed to be the same (actual metal on plates, their proportional thicknesses, the distances of the plates, etc.), then from a discharge perspective there should be no real difference between two 6V batteries and one 12V battery. Alas, marketing hype and the dissolution of the meaning “deep cycle” make this tough to guarantee short of taking the batteries apart and looking inside.
Other factors that are in favor of the 6V include being easier to lift 4 individual heavy blocks one at a time versus 2 heavier blocks one at a time. Additionally, if a cell fries then a smaller unit replacement is possible (e.g. just one 6V versus an entire 12V battery).
I'm also going after a true Golf Cart battery, and in this case it will be a Trojan T-145 6V Deep Cycle. It provides 215 Amp Hours at a 5 hour rate, and 260 Amp Hours at a 20 hour rate. Each battery weighs 72 pounds (eating nicely into our load capacity) and its dimensions match what we have space for.
With the configuration we have, two banks, with each bank consisting of two 6 volt batteries, we will have between 430 and 520 Amp Hours! With our switch out to LED lights, a low consumption electronic devices, and our election to use muscle power everywhere we can (e.g. I'm the windlass) means that we will have plenty of power capacity for our needs between charges.