Recently I disassembled a Nikon lens, the first 24-120 with VR as the VR constantly engaged. The plan was to disconnect the VR unit completly and use, interim, without VR. Didn't work, as apparently apperture control (electronic in this lens) and focus (AF and manual, also electronic) go over the same platine. No VR, that worked, but also no focus or apperture.
Point of the story, the lens had some shims to get into the proper focal plane relative to the camera. The model in question doesn't have the best sharpness reputation, some people put it on the worst 10 list of Nikon lenses. The sample I had is sharp so (VR didn't engage until 28 mm). My theory now is tgat the lens is sharp, and the bad rep comes from compromises during manufacturing (Thailand instead of Japan, with all the corresponding issues of setting up high precision operations in a new site), and potentially sub-par QC. Not sure if other lenses have shims as well, I'm kind of not inclined to disassemble perfectly working samples just to find out.
So no, shims aren't per-se a bad sign but rather one of a certain calibration strategy. If those shims are everywere so, manufavturing quality propably isn't the best.
Oh, one word on 50 mm lenses. Those are among the fastes, sharpest lenses ever regardless of manufacturer. And dirt cheap compared to "pro" models. Seems to be quite well understood optics.
I do have two pre-AF Nikon lenses, and those are master pieces of precision mechanics, dating back to the late 70s and early 80s.