I connect regularly through Munich and it is my favourite airport for connecting flights, it has a very easy layout and good signs. It was specifically designed for connecting flights (Terminal 2 where all the Lufthansa flights are is very new). I know that they routinely allow flight bookings with transfer times as short as 30 minutes - and I would have no problem booking a flight with such a short transfer there. While for Frankfurt I would always want at least 1.5 hours!
On the question about security: I am German and have a lot of experience with German airports and I never experienced a situation were every traveler was subjected to a pat down. I am not saying that this might happen if there is a special security alarm, but it definitely is not standard procedure. I am very good at avoiding wearing anything with metal on my body, so normally I pass the metal detector without any sign and if this is the case, I am free to go on. Also, Germany does not require you to take your shoes off.
And finally, CPT Tripss: it was nice to read a few lines from the expert! If you are in contact with her, please tell her that I say hi! I miss her posting here!