I have read that the infamous Drake Constitution passed just after the war DID disenfranchise men who served the Rebel cause, and required an oath of allegiance for many things including holding public office and voting.
My thinking is not so clear about Union troops preventing southerner sympathizers from voting. I know that at some elections Union troops guarded the polls to ensure that voting was conducted without intimidation by southerners and to keep order. I read of this in some Union army reports in the "O.R." I also know that the mere presence of Union troops at some Missouri polling places intimidated southern sympathizers. I have also read that the use of the Australian secret ballot was not used in Missouri until some years after the Civil War, so how a man voted was a public matter. Since how individuals voted was such a commonly known subject, I can see no need for Union officers to seize voting records. Besides, issues were not always split along north/south sympathy lines.