It happens to me with Fats ans level 56+ missions. In lower levels they're plentiful (I can kill 20 in a single mission), but in the highest-level areas they are nowhere to be seen. I can kill 1, maximum 2 every mission, and sometimes I can't find a single one in the entire mission. It also happen to a lesser degree with Riots, but only because "HERC Riots" don't count. In the other hand, in lower levels (40's I've sruggled with HERC, but in level 56+ missions I can get 20 of them without effort.
So it seems that every zone or level tier has different "rare" zombies. As for the question if it's intended or not, i can't really say.