according to the machzor vitri why should we still be saying the tefila of yhe shmei raba when the bais hamikdash will be built (days of moshiach), like is mashma from the gemara ashrei hamelch... but when moshiack comes we will destroy amalek and hashems name will be full kavyachol
Marcus Abisror, Long Branch
Shalom,
I will have to look further for additional sources on this, but at the moment I can share with you that there is a discussion in the Beis Elokim of the Mabit (Sha'ar 3, Sha'ar ha'Yesodos, chapter 61) that relates to your excellent point. He notes that reciting Kaddish would have been possible "even in the times of Moshe Rabeinu because Hash-m's throne was not complete because there was Amalek." The implication being that in the future era of Ge'ulah it would not be relevant.
May you continue to attain greatness in Torah and Yir'as Shamayim!
Bi'Verachah,
Yishai Rasowsky