I did not know that about the 1890 census. That's actually helpful as I was confused as to why these people just disappeared for 20 years.
Here is a summary of what I know about this set of great-great-grandparents:
Frances Wagner, the wife of Nathaniel Wagner, was born in May 1854 according to the 1900 census, and had been married for 19 years, putting the year of marriage around 1881. According to the same census she was born in Pennsylvania.
According to the 1880 census, Nathaniel was living in Lindley, New York. The next mention of him I have found was the aforementioned 1900 census, when he was living with his wife and daughter in Avoca, New York.
My great-grandmother, their daughter, Jessie, was born in either 1885 or 1886, in either New York or Pennsylvania, depending on which census you look at.
I've been hoping to find something that references the maiden name of Frances Wagner, but I've not been able to find any death records for her, nor marriage records for Nathan, or even birth records for Jessie. Since I have no maiden name I have no idea who to look for before her marriage to Nathan in the early 1880s. It's possible there was much moving back and forth across the New York-Pennsylvania border, but so far I haven't found any data on ancestry.com to fill in the missing information.