They do on all other sites AFAIK and I'd like to be able to do some of the things that I'm currently unable to do - my reputation is an unfortunate 7 at the moment.
As long as one of the accounts has more than 200 rep you'll get the bonus. You can only get the bonus once per site, so if you're on 3 sites (A, B and C) and A has > 200 rep. When you associate A -> B you'll get 100 points on both A and B. Then when you associate A -> C you'll just get the 100 point bonus on C. Associating B -> C is effectively done by this point, but wouldn't get you any more bonus points anyway.
You've now got over 200 rep on Programmers so if you break the association and remake it you'll get the 100 point bonus.