I just want to make sure a shimmed neck isn't the sign of other problems and won't affect anything adversely.
That really depends on how far out it is. And is it a bad neck pocket or was the heel of the neck ground too thin? Either way if it is out more than 1 or 2 mm then I would seriously consider swapping it for another one. Shimming does not hurt anything. But a large enough shim job is more than noticeable. I would bet these guitars are not made to really tight tolerances. Play to the masses so to speak. Some people like their action high. I believe SRV kept his a little higher than I would like.

All of that being said. Have you considered replacing the nut? Maybe it was grooved too deep.