I think they can sew up the hide and cover up a hole as long as it isn't too bad....that or it will leave a scar or bare spot and You can show exactly where You shot Your Deer!
For the most part the Taxidermist will skin out the hide and send it off to be tanned and only the portion of the Skull where the Antlers are will be used on the Deers Form.....so a damaged or crushed Skull may not effect the finished Mount!