as a buyer: i really dont mind if an item has a hole punch in the barcode or a cut in the spine because it doesnt really take away from the main artwork. just like Cashflow, i dont like how cover inserts have cut corners/hole punches on the front where it's noticeable. so with that said, if the hole punch is in the barcode, i'd still offer the same amount of money as if it didn't have a holepunch. BUT if the hole punch is on the front cover then i would lower my offer/bid.
as a seller: i don't see a difference in prices when selling RARE items with hole punches in barcodes or cut spines. seems like buyers are only worried about bootlegs, tab marks, and scratches. with that said, every time i sold a rare item with a hole punch in the barcode it always ended around the same price another seller got for their Mint copy. but i guess it really depends on how rare the item is.