Yup. Most of the scripts now have their license info recorded with the script owners' database. So it is easy to track down those nulled copies.
Apart from that, sometimes when someone extracts a nulled copy of a script, they also have a file like say 'Nulled by - XYZ.txt'. So the server owners can catch the website owners running the nulled scripts through that. And of course, complaints. When we get a complain, we check that up and take the action.