I filed this issue with dynmap, but they say it is a VNP problem.

Vanishing properly marks you hidden on dynmap, but unvanishing does not automatically show you on dynmap. You need to manually issue '/dynmap show'. It would be nice if vanish and dynmap states tracked.

Also, in dynmap, the count of players on the system includes vanished players. According to the dynmap maintainer, they are using the standard bukkit api to get this info. I have ProtocolLib installed, which does cause the pre login server list to properly hide vanished players from the count. However, it does not seem that ProtocolLib+VNP hides vanished players from the API that dynmap uses.

First issue should be fixed in dev builds. Second issue I cannot help, nor can they at the moment. In the future Bukkit may add support for what we need :)