T., does your son's extra pinkie seem to get in the way or bother him (like does it catch on things and pull it, or does he function well with it)? If not, I personally wouldn't worry about it and let him decide one day. The only other reason I'd get it done would be if the dr. said that the procedure would be more difficult on him as he gets older (I'm thinking specifically of tonsillectomies).
My daughter was born with a restricted frenulum (tongue-tied). I wasn't able to breast-feed; good thing for the bottle. We went to a specialist who told us that it can hinder a child's ability to physically learn to speak, so because of that we had the frenulectomy to 'clip' her tongue. If they'd said it didn't matter one way or the other, we'd have left it alone.