The family is also in the same area in both the 1881 and 1891 Censuses, and the place of birth for John Daniels is consistently shown as Southwark, Surrey.
1881 Census - Southwark St George Martyr - Borough Road - District 6
Address - 5 Princess Place, Southwark
John Daniels - Head - Mar - 39 - Boiler Maker - b. Surrey, Southwark
Susan Daniels - Wife - Mar - 36 - b. Surrey, Southwark
John Daniels - Son - 17 - Printer - b. Surrey, Southwark
William H Daniels - Son - 15 - Printers Boy - b. Surrey, Southwark
Susan Daniels - Dau - 13 - Scholar - b. Surrey, Southwark
Alfred Daniels - Son - 10 - Scholar - b. Surrey, Walworth
Benjamin Daniels - Son - 8 - Scholar - b. Surrey, Bermondsey
George Daniels - Son - 5 - Scholar - b. Surrey, Southwark
Jane Daniels - Dau - 1 - b. Surrey, Southwark
1891 Census - Christchurch - Christchurch Southwark - District Blackfriars Lodging House
John Daniels - Married - 50 - Engineer - b. Southwark, London
1891 Census - St George the Martyr - Kent Road - District 14
Address - Townsend Street, Southwark
Susan Daniels - Married - 48 - London, Southwark
William H Daniels - Son - 25 - occ. Z___?? - London, Southwark
Susan Daniels - Dau - 23 - Fancy Box Maker - London, Newington
Benjamin Daniels - Son - 18 - Coachman Groom - London, Bermondsey
Jane Daniels - Dau - 10 - Scholar - London, Southwark
I also have all the birth certificates for the children (apart from William H, which I can't find for some reason) and they all show Prole as MMN. I just find it strange that there's no record of a John Daniels that fits prior to the wedding in 1861. I could imagine maybe a missing part of the Census for one year but not multiple Censuses.
Anyway thanks again for the replies!