Hi. Just read this while having toast and marmalade - how English!!
To set yoiur mind at rest, I have a LOT of instruments (not as many as Uwe - Bows gracefully!!)
and every now and then I take necks off for overhauling.
Trust me - I have found more than 50% of them with factory shims - usually a thin strip
of Nylon or in some cases sandpaper, with a heavy grit, stapled to the neck FROM THE FACTORY.
I am certain they are factory, as they all look the same.
This is off an early 80's Ibanez Blazer - cracking bass - stripped for a full overhaul and
stuck to the neck. . . . . Standard issue Ibanez shim!
I could show you loads of examples, from all sorts of makers.
From my experience, Fender have no problems with shimming necks - for them, along with other
maufacturers, it is standard proceedure.
I have also seen shims front and back, as mentioned by Dave W.
How high is your action at the 12th, with just a rear shim?
Cheers.