The main reason you're seeing the increased hits for ubbthreads.php is this. In prior versions ubbthreads.php was just a script that was called to display the main forum list. In this version everything goes through ubbthreads.php. It's our core script that is used for everything. So, before when you're adding a post you'd see a call to addpost.php. Now, it still calls ubbthreads.php with a parameter of ubb=addpost. So, the increase in that area is normal.
It's true that if the shoutbox is used as a regular chatroom it can definitely eat up some CPU. It's not written to be a full fledged chat room, it only has a 30 second refresh, with no way to force it to refresh other than loading the page. But some people will try and use it that way. Perhaps we can put a word of advice when enabling it that it could cause higher loads if people are trying to use it as a normal chatroom.
For example, here. We have it enabled, but it's only used here and there, so it causes no issues.