There are two direct trains Nuremberg-Prague and two direct trains Munich-Prague. The trains from Nuremberg have connection from Munich in Schwandorf and vice versa, so there is actually four daily train connections between Nuremberg/Munich and Prague.
The train is considerably slower than bus (5h15m train, 3h45m bus), because of slow and curvy railway line over German-Czech border. This can be, why the DB timetable shows only bus connections. But the train trip is more pictoresque
You don't need any reservation to this trains, they are not overcrowded even on peak days.