Do the 'number of battery' calculations take into account the DC bus voltage? i.e. if the bus is 12V and the batteries are 6V you would need twice as many

If the DC bus voltage is 12V and you are using 6V batteries, the number of batteries in the battery bank must be some multiple of two. I'm not sure what you mean by "twice as many". HOMER does not know the DC bus voltage so it does not place any restriction on the number of batteries in the battery bank. It is up to you to ensure that the possible quantities of batteries in the battery bank are physically feasible.