Len and Larry,
I am no more of a horse expert than I am a weapons expert, but please allow me to steer you back to a better understanding of the horses used in guerrilla wafare in Missouri. In fact, the opposite of your assumptions is the truth.
The guerrillas obtained mounts and remounts from their friends, family members, and admirers. Often, too, they simply took good animals from anybody. A horse owner found arguing of little use to someone taking his steed who was armed to the teeth. Missouri was rich in horses, especially in the first year or two of the war, and the guerrillas made it their business to ride the very best for their own preservation.
I can think of two factors which left the Union forces with inferior animals facing the better-mounted guerrillas.
One is the often infuriating way the U.S. government bid out for horse purchases. I don't mean that the Union side always bought animals from the lowest bidder, but often that was exactly the case. Sellers learned quickly to offer the Union only the quality horses they would accept--and not any of better quality. Purchasing in large quantities often excludes the finest animals. Some of you who have attended livestock auctions may have seen that.
The second and greater reason for the Union cavalry in Missouri to have inferior mounts is the grinding character of conducting a war in which you wear down your horses looking for an enemy that doesn't want to be found. Even if Union cavalry started with the finest horseflesh money can buy, after a few months chasing wills-of-the-wisp around the countryside your fine steeds are worn down to nags. Sadly, this is why our service people in Irag and Afghanistan are running low on operable vehicles to conduct their own war. Add to this indifferent care of the animals or even outright neglect, and many of the troopers were put afoot. Also, the Union cavalry manning scattered posts across trouble areas of Missouri were forced to push their tired animals while performing duty as couriers, gathering forage and lumber and whatever, escorting supply trains and refugees, and a myriad of other duties that a small post had to perform in order to remain a viable force when the enemy DID make a brief appearance. By 1863 and 1864 some small outposts were hard pressed to field even two to five healthy horses for patrol duty or details. Such a small patrol was little more than bait to energetic bushwhackers.
Based on these conditions, guerrillas may have passed over captured Union nags to choose from civilian horses in the neighborhood.