When I think about 2 x 6 volts vs 2 x 12 volts I think about failure mode.
If one 6 v fails you're in the dark. Not likely, as golf cart batteries are well made to be subjected to abuse.
If one 12 v opens, you still got power. If it shorts, (not likely) you are in the dark and there may be smoke.
If you're gonna rip out the whole thing, I'd go 2 x 6 volts. In either case you want 2 of the same exact type, manufaturer and even lot to have your batteries evenly matched as possible.
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