If my wife becomes Canadian after getting a TD visa to the US as a PR of Canada does she need to get a new TD visa or can she continue to use her third country passport?

Your wife does not need to obtain a new TD. If during the term of your current TN, she leaves the U.S. on vacation, upon re-entry she can speak to the Immigration Officer and may be able to obtain the TD on her Canadian passport, but it is not critical nor necessary. When you renew your TN, she can obtain a new TD visa on her Canadian passport.