I live in Lincoln, so about 50 miles south of Omaha. I think a crucial point left out by the author here may be the massive (at least perceived) demographic disparities between Omaha and Council Bluffs.
Council Bluffs is a vastly less financially successful city than Omaha with far more visible opioid problems.
That is to say, as a local, I don’t know if I would associate the term as much with demeaning “hillbillies or hicks” but more for the socioeconomic and drug disparities between the two cities.
I don’t know if the drug disparity is so large between them, but it certainly feels more visible in Council Bluffs. Maybe why we don’t see the -tucky suffix used as much with other twin cities is that St Paul and Fort Worth are still quite successful metropolitan areas in their own right.
Cincinatti has the real Kentucky across the river. I wonder what that's like. (The reverse could be said as well, and I haven't been to Cincinatti but I'd like to go some day, partly because I saw the Kaufman movie Anomalisa which is set there, and I made a point to check out Schenectady from another Kaufman movie and I was glad I did.)