Yes, their influence count towards matching. 

Clans usually expell members who are inactive for a couple of weeks or more.  After all, they will probably be able to rejoin should the period of inactivity prove to be temporary.

Though it might seem to make sense to do so, a lot of clans don't, possibily because they don't want to appear weakened, loose status, or the experience points, which might be a consideration, in regards building the stronghold, or now when there is the set minimum in order to play the CvC.

My Clan expels inactive members who have not notified Chief of Elder why, but invite them to re-join when they can be active again. That way we have a better chance of avoiding mis-match in CvC events as their would influence count but they are not earning points in the event.

As far as I am aware Plarium does not remove dead accounts so their influence still count in kingdom events and can be a pain especially in KvK if they still have troops left.