Not sure why you say that. Having read a great deal of both I can
confidently assure you they are deeply related. Nietzsche doesn't use
process notation or equations for calculating closed loop feedback
gain. Shannon, Wiener or Weaver don't directly address the question of
whether the cultural software of our society lies within its
institutions or individuals. Nonetheless they are both talking about
the same subject - one that is highly apropos the precarious situation
we find ourselves in today with respect to our failing social
cybernetics.
Sytems engineering, as a engineering discipline, is treating other things than Nietzsche did. Unless you go to philosophical meta questions about "systems", I have yet to encounter those in real life.