Wow, Althea, those are two super important points.

(Just brainstorming here:) what scenarios do you think could occur in the late 1800s whereby a husband is alive but his wife would technically own property?
Would she automatically get the property if he abandoned the family?
If he was missing presumed dead? (You'd think with a well-known family there'd be mention in the newspaper of that though?).
What about something rendering him incapable, such as illness, or imprisonment? (The latter you'd also expect to find some court case esp. if he's away for years). I wonder how long John was in Auckland Hosptial for?
I also have found a couple of new things re: Duncan McPHERSON, City Missionary (on John's death certificate).
Firstly, this sheds more light on the actual role of this City Missionary:
http://www.presbyterian.org.nz/archives/Page181.htm"Duncan McPHERSON... Appointed to the Auckland Presbyterian City Mission in 1884, visiting door to door, finding out the lapsed Presbyterians and the children not attending any Sunday School, also the Gaol, Hospital, Veteran’s Home, Mental Asylum, Hospital, Nurses’ Home, and newly arrived immigrants. Acted as Auckland City Missionary for 29 years."
Secondly, there's a chance that Duncan McPHERSON may have actually been known to the family.
For example, here is Duncan McPHERSON involved with St. James Presbyterian Church, Pollen Street, Thames in 1889:
http://paperspast.natlib.govt.nz/cgi-bin/paperspast?a=d&d=THS18890513.2.9&l=mi&e=-------10--51----0burnley%2C+lancashire-allWe also have "Mrs LOUGHLIN" in the Index of Names (1872-1894) in "Seat Letting Cash Book" of the same church:
http://freepages.genealogy.rootsweb.ancestry.com/~babznz/stjameschurchthames.html)
So Duncan McPherson: was he visiting the Hospital by coincidence when John died? Or was he a family friend or minister? Was he the one who provided the birthplace & length of residency in NZ? Or did the Hospital? John's accent might have made the birthplace obvious, but how would someone else know the length of residency? Wouldn't it be easier to know or find out the name of his wife & kids?
Which makes me wonder: could it be possible at all that John's family intended to complete the rest of the details on the death cert, but for some reason didn't? Did the family rely on someone like Duncan McPherson to take care of the paperwork for them? Is Eliza Jane mentioned on the certificate? (Just thought also, as for his parents, maybe she didn't even know who his parents were).
Lindy -- I think one next step (just a suggestion) might be to go ahead and contact the Waikumete Cemetery to see if they hold records on who purchased John's (Presbyterian) grave (& also whether he's buried with anyone). What do you think?