The thing here is that we seem to know that mother Nellie just plain did not marry.
When a person's parents were not married, it was very common for them to make up a father's name for a marriage certificate. (The same was true for people who were using a false name when they married, as my gr-grfather and his sister did.)
There were standard reasons for the name given, some of which have been mentioned. It could have been:
- the name of the person's maternal grandfather
- the name of the person's maternal uncle or older brother
- the given name of the person's stepfather (mother's husband or partner) combined with the person's own surname
- the given name of the person's real father (if they knew it) combined with the person's own surname
- in the case of a man, his own name and occupation (making him a Jr following in the footsteps of a fictional Sr)
- a complete invention
The same applies if an occupation was stated: it could have been the real father or stepfather's occupation, regardless of how the name itself was concocted. Or, again, a complete invention. I don't think I saw the answer to what info was given in this case: an occupation or "deceased" ("deceased" being the easy out, especially if the person marrying was not telling their spouse the truth either).
The birth certificate is likely going to show a blank (and all else is pure speculation until you have it). Then it's a matter of searching for clues -- if there is a James with the right occupation in the vicinity or with some family or occupational connection with the mother or with her father, when the child was born, for instance.
Some mothers in this situation left clues and passed on information -- my great-aunt's middle name was the surname of the household where my gr-grmother was in service, as an example (and this was fairly common practice), and the story passed down by my grmother is that her sister's "father" was the son of the head of that household.
Without such clues ... it will likely indeed be paddle and creek time.