IMO
Instruments, generally, are all different, even 10 of the same model, made by the same factory, will vary in some small way. Even premium products, certainly not just affordable ones, need tweeks sometimes, to the neck, the electrics or whatever to get them just how you want them. An other variable of course is the player themselves and their requirements.
I see no problem with a shim, if it gets the instrument how you want it.... IF you know what you're doing.... AND it's actually required and not just bunged in for the sake of it.
So I agree with the OP , when its not necessary its obviously been done by someone "clutching at straws" rather than knowing what they're doing, how ever I'd rather that, than filing or cutting stuff out.... at least a shim is reversible, anything more drastic isn't.