If I have found the correct Mary & Susan it is doubtful that they belong to this couple as the Frances given as the mother is Frances H or Frances Henrietta
Benjamin and Frances married in 1847 at the Scots Curch in Sydney and the one child whose baptism is in the records(1851 Alfred C, seems a likely child)was baptised at St lawrences C of E - so they didn't seem too concerned as to which church they went to & may have simply not baptised the children - or the records are lost. In 1856 there is one civil registration for Benjamin H. Perhaps there were no more children after this date, given that they did register Benjamin. Could they have moved interstate.
Do you have a death certificate for Benjamin or Frances - this should contain - at least - the number of children they had - not necessarily the names, depending on when they died. The birth certificate for Benjamin (1856) could give details of previous children.
I can see a possible death for Benjamin 1880 - but not for Frances.