We usually have at least one NPC in charge of watching the draft/riding animals while the PCs are off doing their adventuring thing.
In my first campaign, it was Old Clem, a 60-something fisherman who figured out watching a band of PCs' animals was a lot more lucrative than fishing for a living. He used to send letters back to his fishing village detailing the PCs' adventures, yet somehow giving the appearance that he was their leader, not their hireling.
In my next campaign we ended up with the NPC little brother of one of our elven PCs. As he had a thing for our female elven ranger, we didn't ever have to worry about him leaving with the PCs' mounts. (They even got married at the end of the campaign.)
In our current campaign, the PCs just hired on a half-orc commoner NPC to look after their animals. Since he's a bit of a drunkard, he's the most sketchy of the bunch but so far he's been on his best behavior, also realizing this is a much better gig than he had before. (He was serving a jail sentence for a crime he didn't commit, so he's pretty predisposed to loyalty toward the PCs.)
Johnathan