I love it when a plan comes together!! I didn't think to look before, but there are a couple of people with trees on Ancestry for Mary Ellen MIDDLETON and Daniel HAYES. Mary born c1820 in Liverpool - children with Daniel are Mary (1849), John (1850), Sarah (1854), Thomas (1857), and Robert (1858). Mary might have been James' daughter, not Daniel's. Daniel died in Forbes in 1892, and Mary in 1899. It doesn't look like Daniel and Mary married.
So this scenario would certainly explain the confusion over the different surnames. I don't buy into father James being deceased though, I think he just went to the shops one day and forgot to come home!
I would be confident that this is sorted, but the only other thing you could do is to get Mary's death cert. It is a bit of a gamble and depends on the informant's knowledge but I would at least expect to see Susan named as a child.