I don't know about Munich, but all of the Catholic churches in downtown Frankfurt have Mass every day, and sometimes 2-3 times per day, and Frankfurt isn't anywhere close to being overwhelmingly Catholic, as any town in Bavaria might be.
There are other bike tours in Munich that seem to be getting better reviews than Mikes Bikes. If you are a non-biker though, why go on a bike tour, when you could go on a much more informative and accurate walking tour?
Stores in Germany are always closed on Sundays, except for on random Sunday Shopping days, and stores at main train stations, airports and souvenir stores near major tourist attractions. Museums tend to be closed on Mondays, as are some restaurants.