As far as the connection in München Hbf goes, 12 minutes is more than enough to get up from the S-Bahn station to your CNL train. It is a bit of a walk: S-Bahn is located at the north end of the main station, while the CNL train will probably depart from near the south end -- but again, 12 minutes is fine. The Munich S-Bahn does sometimes run a bit late, but at that hour I think you'll be OK.

Since Switzerland is now in the Schengen area, you won't have to clear Immigration. Do you have checked baggage? That is also usually fast at MUC, but it is variable. If you only have hand baggage, then your connection should be fine.

Of course, if your flight from ZRH to MUC has a major delay, all bets are off!