I've done it both ways. With barely halterbroke weanlings they have gone 16 hours straight. Took all the partitions out so they had the run of a 4 horse. With the others, I've always stopped somewhere that I could get them out for the night. I had a 2 year old shipped from TN to CO via Chicago and he was here in about 36 hours. There's no way he ever got out of the trailer. Can you remove a partition or tie it open to give him more room? It will also help with more air so it won't get as hot back there. If you know that if you let him out, it will take 2 hours to get him back in, leave him in. You can't risk the chance of him getting away from you if he starts throwing a temper tantrum. It's not worth the stress on both of you. It won't kill him and if he can move back and forth, you won't get the stocking up. If you stop and untie him so he can drop his head he'll be fine.
Hey do you think it's a horrible idea to take him that far without getting him out at all? My vet mentioned just stoping for a an hour or two give them a chance to relax. What do you do on your long trips?