Upvote:1
There should be no meaningful change in the S-Bahn schedule due to Oktoberfest, but lookout for any posted notices.
Exit controls and screening should take <30 min (my last experience was <10 min actually). This will depend on any expedited queues you qualify for.
For clarity, there might be additional, but not necessarily separate checks. I departed MUC right around all the recent hubbub and 'security' was only slightly more theatrical than usual, lots of swabbing and extra dower screeners.
You best be may be to just ask an airport official how long it takes to enter the terminal around 1330 and make plans from there.