One would think that if the vast majority of folks in Kentucky and Missouri were pro Confederate then said states would of been Confederate. Certainly Dyer's Compendium does not reflect that the majority of white men in either state flocked to the Confederacy more then the Union.
The figures I have seen from the Missouri Historical Society is approximately 30k Confederate vs 110k Union. Per Historian Steve Freeling Kentucky is 25k Confederate vs 50 k Union. Both figures exclude USCT,guerrillas and Militia.
Yankees had the numbers to military control those states. They wanted to be independent. Majorities in all upper south states were unionist. Influence can change perception.
Maryland a good example. One of the first battles of the war was when Yankees paraded thru Baltimore. Federals stole the ballot boxes, militarily took the State. First state to enter Reconstruction. Same thing happened in West VA. If Lincoln could of gotten troops into East TN, they would of take it.