We study fixed points of iterates of dynamically affine maps (a generalisation of Lattès maps) over algebraically closed fields of positive characteristic p. We present and study certain hypotheses that imply a dichotomy for the Artin-Mazur zeta function of the dynamical system: it is either rational or non-holonomic, depending on specific characteristics of the map. We also study the algebraicity of the so-called tame zeta function, the generating function for periodic points of order coprime to p. We then verify these hypotheses for dynamically affine maps on the projective line, generalising previous work of Bridy, and, in arbitrary dimension, for maps on Kummer varieties arising from multiplication by integers on abelian varieties.