I don't think you have to clean up the images for use in vectorizing. You might even lose details cleaning it up.
An example of this is the Galaga sideart. Someone cleaned that up but in doing so replaced the top logo with a flyer image (quite a different logo) and removed all the shading patches in the ribbon (replaced all greens by 1 color). It might look better visially after cleaning, but when you vectorize it it it doesn't need to look clean. As a result the vectorized art based on that image is now wrong too.
It would be nice to know the original colors though. Often the colors in pictures are way of. In fact I just bought a galaga kickplate and the colors are so different to what I thought they would be. I took a picture of it and amzingly the colors came out like in all the pictures I saw on ebay. Apparently digital scanners and camara's are really bad at capturing color accurate pictures (at least with respect to the super bright colors used in arcade art).