You asked, "What about Henderson Hill, were all those POWs listed on a federal register somewhere?"

Good point. Their website reports 100 men of the regiment were captured. However, none of the records for men of the regiment contains POW information. It seems very likely therefore, that your Dr. Smith wound up at Camp Morton as your information records.

See: http://www.acadiansingray.com/2nd%20Regt.%20Cav.htm