OP, I work in medical developmental genetics (and study things like polydactyly) so coming at this from a pseudo-clinical POV.
Firstly, try not to take to heart questions about a potential familial relationship between you and your DH. It's a standard question when assessing children with genetic anomalies. Answers are used to guide future counselling etc, and may highlight the precise nature of the genetic anomaly, but it carries no judgement.
Secondly, in my opinion, the foot surgery is a no-brainer.
Thirdly, to echo another poster upthread, does he really have a fully-formed and functional extra digit (including metacarpals - the bones under the back of your hand)? This would be called Type A ulnar polydactyly, and would be more complicated to surgically correct than a simple "extra nubbin", requiring bone reshaping, transfer of muscle tissue, moving ligaments etc. My reading suggests that this operation is best done early.
It's a really tough choice. I tend to agree that in day-to-day life, most people won't notice. It took me more than three years to notice that a school friend of mine had a missing finger (I was about 14 when I first realised, and obviously it was a non-issue in social terms). And yes, children can be cruel. But also, they are remarkably accepting of difference in most cases, more matter of fact than adults might be. A lot of education (and our world) is to the base 10, possibly because 10 fingers is the most common number, so there will likely be a lot of stuff that your DC will have to adapt to, because it simply won't occur to people to adapt for him. His nine times table, where you put the finger down that corresponds to the multiplier and count the fingers to the left (tens) and fingers to the right (units) might require a workaround
.
Of course, many clever maths people think that a duodecimal system, to the base 12, is far better than our decimal system. It is definitely the base of computing, so your son is symbolic of the future of civilisation right there. Polydactyly is seen in some cultures as a symbol of supernatural power, so he could well be a god in some countries. And finally, given the extreme usefulness of our fingers in the evolution of humans, maybe polydactyly is the way forward, and he's a more highly-evolved being than us Five Fingers (nobody bite, I know that's not the way evolution works...).
I came here to say operate and remove, but I think I've talked myself over to the other side.