I would not be concerned. When you log into CB the phpbb Connector plugin goes thru the steps to log you into phpbb as well. They still act as 2 seperate programs. So if you only want your users to log in or out with Joomla/CB then I would hide the login and logout links on the forum. But this is not essential. Same goes for registration and profile links. They can be maintained seperately if desired. The only catch here is that once linked in the connector... any changes to the username, e-mail, or password (sometimes avatar) will update both phpBB and CB. In the newer alpha version you have the ability to disable parts of the plugin... not that this is what you are looking for...
Short answer... for me... I would probably hide the login and logout... but it is not critical and nothing will get messed up if they logout of phpbb and in (to phpbb) as someone else while being logged into CB... nothing to get messed up.
Greg