According to at least some (modern) sources, only partially by Isaac, but not entirely, even though Isaac's name was attached to it from its earliest surviving source. (Burn, David J., Heinrich Isaac and his Recently Discovered Missa Presulem ephebeatum, in ""Recevez Ce Mien Petit Labeur": Studies in Renaissance Music in Honour of Ignace Bossuyt" (Leuven University Press, 2008), Mark deLaere and Pieter Bergë, editors, pp.51–52 (noting an article, Heidrich, Jürgen, "Heinrich Isaacs (?) Missa Carminum (from Heidrich's site: Heinrich Isaacs(?) ‚Missa Carminum‘: Überlieferung – Werkgestalt – Gattungskontext, in: Jahrbuch der Ständigen Konferenz Mitteldeutsche Barockmusik 2001, Schneverdingen 2002, 123-139.)
According to German Wikipedia, the music of Agnus III was reused for a piece Bruder Conrat.