Thanks for the response.
I get that it's perfectly fine, and common to use them during set up. Phobia? Not quite, but it does make me doubt the quality of instruments coming out of a factory if they have to use shims to compensate for design or workmanship flaws on a regular basis.
Sometimes the shim is part of the design, and luthiers use them as well. Those don't worry me. I am referring, for example, to a standard J-bass copy, designed to have the neck bolt directly into the pocket in a perfect fit, and the assemblers are having to add shims on the regular. That speaks to a process flaw.
I have owned Kawai, Fender, FGN, Michael Kelly, Ibanez, Squier, and Offbeat bolt-on basses. I prefer bolt-on necks specifically because they can be replaced, shimmed, modified, and removed during refrets and more serious work. I have removed the necks on all of those, except the Offbeat, and never once did I find a shim. I have had a shim added (the Kawai) but none of them were shimmed by the manufacturer.
So, like I said, not anti-shim, but assemblers having to use shims to compensate for design or workmanship flaws - that makes me wonder what else they couldn't get quite right.