Accepting a community wiki answer to a non-CW question does not result in 2 additional reputation points for the accepting user, as it would for accepting a normal answer (see e.g. Why doesn't accepting a CW answer for a not CW question give reputation? and CW answers considered harmful?).
I don't see any reason to handle CW answers any different that other answers in this regard. The idea behind the acceptance bonus doesn't change for CW answers, there is no reason to deny users the bonus here.
There might be some borderline cases when the accepting user also participated in the CW answer. If he created the CW answer, he should not get the bonus, but in all other cases I think the acceptance bonus should still be payed out.