Some speculation to consider:
Humphrey,the grocer,appears at other times to be Humphrey the boatman.I assume you have them,but in reverse order the census references are
1891 4642 127 36 (2,Aber Place) "Boatman"
1881 5547 7 8 (1,Aber Place) "Grocer + C"
1871 5692 5 2 (High Street,Llanaber) "Grocer & Baker"
In 1861,solely based on the presence of the son John(1860) indicating the same family,his wife Jane,given as a "seaman's wife" may be at
1861 4320 56 15 (Glanaber Street,Barmouth)
and maybe Humphrey at
1861 2738 50 1 (West Derby,Lancashire--"Jane and Elizabeth" Smack Coasting)
Similar name to William's vessel,but Humphrey is given as born Penryn,Merionethshire.
However,if the Jane above is correct,the presence of a daughter Ann Lloyd Jones,suggests the marriage is Humphrey Jones/Jane Lloyd in 1854.
The father of this Humphrey Jones is given as John Jones,mariner.
There is a John Jones,mariner,with wife Jane,"next door but one" to Mary Humphreys in the 1871 census and "on the rock" in 1861
1871 5692 22 36
1861 4320 53 10
If these are Humphrey's parents and the term "nephew" has it's current narrow definition,Mary Humphreys(married name),should be sister to one of these.As Jane is given as born Trawsfynydd,perhaps it is more likely that she is the sister of John Jones(Barmouth)
I can find one such possible combination that could fit the bill:-
John(1794) and Mary(1803 or 1804) born Llanaber to Lewis Jones and Gwen his wife.
Obviously all very speculative,and still no marriage of William Humphreys to Mary(Jones?) that makes any sense.
Regards
Roger