Rail Travel within, into, and out of Germany w/ refugee situation

Certain border areas may have some refugee rail passengers but your routes should be unaffected. Refugees aren't traveling from Berlin to Munich or from Munich to Zurich or from Zurich to Frankfurt, and they probably aren't paying for the more expensive high-speed trains that you plan to use if they're using trains at all. I never bother with seat reservations unless it's a major holiday. Enjoy your trip.

Remember you will be in first class with your Eurail Select Passes. It is unlikely that many refugees will be buying first class tickets.

and seat reservations from Berlin to Munich are ~50 Euro/person alone,

When I go to the Deutsche Bahn webite, the seat reservation for this train is 4.50 euro per person. Where did you come up with 50 euro?

I had been using RailEurope.com through RickSteves'. Didn't realize until now that the price it gives is total for the party, not per person! We plan on getting off the train in Bamberg for a few hours to break up the trip and get lunch. Looks like $6/person from Berlin to Bamberg and $6/person from Bamberg to Munich. Much better! We may just book reservations for peace of mind.

FYI, the DB site will sell you seat reservations (reservation-only check box) within Germany, but not on the international route. RE will sell it, but probably have to ship it to you, not an e-ticket (they'll tell you before you check out). Probably the easiest solution for reserving that leg, if you want to, is at a train station, such as the one where you first have the pass activated.

RailEurope will charge you $6 per leg, $12 for Berlin to Munich with one change. However, on the German Rail website you can book both reservations, Berlin to Fulda?/Nürnberg? to Munich for one 4,50€ (~$5) charge.