Clear and paint gets old. The trouble with NOS is that it's been boxed up for 20 to 40 years and hasn't been beaten on by steel balls for the entire time. This can make the paint a bit more fragile and prone to crack. During the time, insert plastic shrinks and causes cupping, or insert sinking. A clear coat can fill in the inserts and protect the paint.
As far as touching up goes, that depends on the particular playfield, but I know in a recent case my NOS playfield had some yellowing I had fixed up prior to clearing.