Just my opinion, but as to how it will effect the value is as follows:
Take the asking price of the gun, subtract the cost of a new barrel, installation costs, refinishing if needed, and a reasonable amount for the time that you don't have the gun while it is being worked on and you arrive at the value.
Seriously though, I would not buy a gun that has been magnaported unless I could get a SUBSTANTIAL discount. The first gun I fired that was magnaported was a 4" nickle 29-2 with full house loads. The muzzle blast was unpleasent, even with muffs on. The nickle plating around the magnaported portion of the barrel was starting to flake and it discolored the front sight. Also, didn't really notice that much of a difference in muzzle jump or recoil.