IMO it is acceptable to refinish store model bats and in many cases the practice results in a more desireable piece. Of course, you would only do this if the finish is trashed and the bat in poor shape. If anything is added, i.e. a knob repair etc, it can detract from the price of an original example in nice shape, but the value is far greater than that of a damaged original piece.
Fred Lowman is a BRILLIANT restorer of bats. I have sent him bats with shattered handles that he can make new again. It really is amazing.
http://www.crackofthebat.net/home/lesson-format
An exception would be decal restoration. I would not touch a repainted decal bat with a ten foot pole.