Yes, yes, yes -- a horse CAN come up lame after a trailer ride! Last night, my new 12-year old TWH mare arrived after a six-hour trailer ride from W KY, and when I saw her (an hour after she unloaded), she was sweaty, shaking and moved like she had string-halt in her back left. I did a little research and learned that long-distance trailering can stress-out a horse as badly as if it had walked the distance rather than hauled. (I wish I had bookmarked that article, but alas, I did not.) Anywhoo, I spent some time with her this morning, and she's moving perfectly well. (Really spooky, but she moves fine.) I am convinced now that she braced for the entire ride, and her muscles tightened up because of it.
I would def do the x-rays on your horse, but I'm wondering if your horse is sored-up due to muscle tightness? Is it a scrambler in the trailer? Could it have damaged tendons/ligaments by bracing during shipping? It may not be as bad as you think, my friend. Prayers that your new horse recovers soon, and that it's not as severe as you suspect.