You need to log into the site and uncheck the hosts not in use.
One thing I typically do is to re-license all the hosts in the environment, then in the licensing site, look at the last licensed date of the hosts, and uncheck all the hosts that don't have the current date.
Is there a programmatic way to de-activate licenses?
It's extremely tedious when you have thousands of servers to scroll through, just to deactivate a few hosts.
There are no supported tools for this. I've heard of some customers have written some scripts to pass input directly to the licensing page but nothing supported.