No I dont think it does flow deduplication (Im running a version behind the latest so I cant say definitively). It doesn't even have out of the box alerts. They did add NBAR2 monitoring that had been asked by the community for several years into the last release. NTA is a basic netflow monitoring tool. the alerting, flow deduplication, and IP Lookups to Security threat Event feeds you would expect in a NetFlow tool are not in NTA. If you really require these features then you will have to look for them from other tools in your environment or look at another Netflow tool altogether, like Plixer's product line:
Hope that helps.