NinjaSteve,
If the original link was to
http://somedomain.com/track/MzE3doWTf/
or
http://somedomain.com/ttrack/MzE3doWTf/
or something like that which did a redirect to
http://tourdomain.com/?nats=MzE3doWTf
then yes, it will track fine. the nats code doesn't have to be passed in the URL at all, but is often done that way to make affiliates feel warm and cosy. However, like PBucksJohn said, it must pass via the NATS tracking script to set the cookie.