I don't know what you have on Roy but it looks like he is in1915 and 1925 Kansas census, both timeslisted as nephew. - with Uncle A.V. Kline and Aunt Pearl
In 1930 he is in Jackson County, MO
He died in California De. 21, 1954
In 1900 census there is also a daughter Helen born that year. I found her and Roy (listed as Ray) in 1910 Jefferson, Johnson, MO living with grandparents Matthew and Anna Kline and other family. (there is an Albert V. Kline, uncle to Roy listed so likely the A.V. from 1915 and 1925 Kansas)
So it looks like John and Jennie may have died. If so they died between birth of Roy in 1906 and the 1910 census. I tried looking for their deaths in Nebraska, Missouri and Iowa on ancestry.com but did not find either of them.
I also checked on familysearch.org and did not find them there either.
I looked for family trees on ancestry and only found one which does not have death for John - it doesn't even show wife Jennie at all.