Hi.
If done correctly (for the tone) there's no ill effects.
Unfortunately 100% of the shims I've encountered and 98% of the shimming techniques I've seen explained and suggested here at TB are what I consider hack-jobs.
When the contact area between the neck and the body is reduced to two narrow strips, and the wood on the neck heel is stressed and bent with the mounting screws, loss of sustain and uneven frequency behaviour (ie. dead spots) are the result.
If a good vibration transfer (=good, consistent tone IMHO) is the goal, a wedge shaped shim that cowers the whole contact area is the only way. That's also how I do it, unless I put the body into the bed of a milling machine and tilt the pocket by milling it.
Regards
Sam