Are 2 x 6 volt batteries better than one 12v battery?

Well I guess there's a few ways to look at this and considerations.

The largest 12 volt batteries are 260Ah (approx) @ 20Hr rate. 6 volt batteries can be 420Ah as they have half the plates but twice the capacity. So one answer might be yes 6 volt is better if you need 400Ah of battery because you could use two large capacity 6 volts instead of two mid-sized 12 volts. The 6 volt battery at 400Ah is quite often an L16 case size which is tall, these batteries in a flooded battery require the height to store them and also need to be deep cycled regularly to keep the acid from becoming stagnant (see stratification).

From an electrical point of view a 12 volt battery is actually six 2 volt cells in series. There is no difference between 2 x 3 cells (2 x 6 volt) or 1 x 6 cells (12 volt). The physicall size of these cells is quite often an issue for different installations so sometimes one form factor is better than another.

Lastly, if one of your batteries fail in a 2 x 6 volt installation your voltage drops dramatically (normally 2 volts per dead cell) or if there is an open circuit (just like a fuse blowing) the voltage will be zero volts. That may render your vehicle useless. Whereas if you have two 12 volt batteries in parallel the voltage will appear normal but your capacity will be reduced by 50%. This later is harder to detect if you don't have a battery monitoring system because you can't see the capacity reduction vs. voltage.