With that kind of mileage I wouldn't worry about the ball joints, they should be fine. A quick check wouldn't hurt anything just to be sure, but unless they were faulty they shouldn't be worn out. Since the pitman and idler got skipped when the ball joints were done though I would definitely check to make sure the LCA bushings were done, they get overlooked a lot and they can cause alignment issues, among other things. But it sounds to me like the alignment shop doesn't know what they're doing more than anything else.
Have you changed the ride height with the torsion bar adjusters? That's about the only other thing that will throw the alignment out besides bending something or the bushings going out. And even then it should be the same-ish side to side unless the car isn't sitting level or wasn't before.
