I think the two registration numbers are only because of submitted returns one from Hexham and one from StMary's. JM to correct me if wrong

Yes, more often than not the reason for two, and sometimes up to four or five, different reference nos. for marriages prior to 1 March 1856 (commencement of civil registrations) is simply the record of the ONE marriage, being transmitted through the various NSW Chaplains to the Sydney office. Christ Church, Hexham in the 1840s was of course where C P N Wilton was stationed. I have spent some time going through the online images (via Rootschat links, see below), but I have not located that ceremony in the parish register that has been imaged. There were of course at least two registers operating concurrently (one as a back up for the other). While it is at least unusual to find a RC ceremony in a C of E register in the 1840s, it would not be unusual back earlier in NSW Early Church Records (particularly in the decade of the 1810s and into the 1820s). But it would definitely be unusual for two separate ceremonies to be held for the marriage of the one couple, one a RC service and one a C of E service.
The Early Church Records for RC services in the Newcastle district are usually coded LK or LL. The NSW Parliament passed Acts for RC services in about 1834, so these would not have needed to be transmitted via C of E registers, but via RC registers to St Marys Cathedral in Sydney.
http://www.records.nsw.gov.au/state-archives/guides-and-finding-aids/short-guide-4/short-guide-4Vol 121 is shown as " Supplementary Registers - Baptisms,
Burials and Marriages, 1827-1901" (EDIT after reading Dundee's later post ..... I have drawn line through "Burials and Marriages" to better reflect the accuracy of the NSW SRO guide's mention re Vol 121 that I have linked, so please See Dundee's later post re Vol 121 - 123)
There are flaws in the NSW BDM indexes. Perhaps CH has been wrongly coded to this particular marriage.
I will pull thinking cap down a tad harder

BUT if anyone is about to order that document, please please please, do not waste your pennies on the real deal certificate, and instead consider ordering an official transcription. In both instances you will only get a typed transcription, and the Official Transcription Agents are cheaper and will send through as an email attachment, and if you order the full transcription, that is as good as the real deal document for family history purposes.
There are in fact at least THREE registrations for that 1844 marriage

Vol 93, Line 2190, Isaac HOLBOROW and Johanna CANTWELL, registered LD
Vol 121, Line 209, Isaac HOLBOROW and Johanna CANTWELL, registered CH
Vol 131, Line 209, Isaac HOBERTON, and Johanna CANTWELL, registered LD
Now, re Christ Church Cathedral, Hexham and the images of the registers there.... Thanks to RChat NSW resources board
http://www.rootschat.com/forum/index.php?topic=369703.0here's the links
Baptisms, Marriages, Burials, Christ Church Cathedral, Newcastle
http://www.flickr.com/photos/uon/sets/72157606066769147/ 1820 1899 Family Register
http://www.flickr.com/photos/uon/sets/72157605008173551/ 1826 1837 Baptisms, Marriages, Burials
http://www.flickr.com/photos/uon/sets/72157604433014652/ 1837 1838 Baptisms, Marriages, Burials
http://www.flickr.com/photos/uon/sets/72157605132739200/ 1839 1861 Baptisms, Marriages, Burials
http://www.flickr.com/photos/uon/sets/72157605674610949/ 1856 1868 Marriages Register
http://www.flickr.com/photos/uon/sets/72157605785759029/ 1869 1885 Marriages Register
http://www.flickr.com/photos/uon/sets/72157605802132868/ 1885 1897 Marriages Register
http://www.flickr.com/photos/uon/sets/72157606197590347/ 1899 1913 Marriages Register
http://www.flickr.com/photos/uon/sets/72157605928662968/ 1913 1914 Marriages Register
http://www.flickr.com/photos/uon/sets/72157606308436455/ 1914 1916 Marriages Register
http://www.flickr.com/photos/uon/sets/72157606323070651/ 1916 1918 Marriages Register
http://www.flickr.com/photos/uon/sets/72157606450662513/ 1918 1929 Marriage Register
http://www.flickr.com/photos/uon/sets/72157606952230042/ 1929 1936 Marriages Register
Cheers, JM