I am using the free version of remote utilities and I normally remove connections by going to remote install, then uninstalling the host. That way I can replace that machine without using another one of my limited connections. However, I cannot do that as I have already removed the hard drives of those machines and cannot put them back together.
It's enough to delete the connection in the address book, there's no need to completely uninstall the Host. The amount of your endpoints is the number of connections you have in the Viewer address book.
Please try to disable showing the Active directory tree. Open the Viewer, click Tools ➝ Options, navigate to the Misc tab and enable the Hide default domain controller checkbox. Please note, that endpoints in your Active directory tree also count.