The bus to Prague no long departs from the north side of the Hbf. It now leaves from the Munich ZOB (Zentral Omnibus Bahnhof), which is located next to the Hackerbrücke S-Bahn station, one stop west of the Hauptbahnhof S-Bahn station.
There are four buses daily, at 7:15, 10:15, 14:15, and 17:00. There are three direct train connections, at 9:01, 12:44, and 17:02.
The trip by bus does take less time than the train, but the train can cost less. Full fare, walk up tickets for the bus, if they are still available just before travel, cost 66,70€ vs 70,30€ for the train. You can purchase Europa-Spezial, bus specific tickets with limited refundability online in advance starting at 29€ per person.
For the 9:01 train, you can purchase the Bayern-Böhmen-Ticket right up to train time from any ticket automat for 26€ (first person, 5,60€ each added person up to five, total). That will take you by regional train to Pilsen. Once you are in the Czech Republic, you can buy a Czech Rail ticket from Pilsen to Prag from the conductor for 100 Kc (about 3,70€) per person.
For the other two trains, due to a recent change in the designation of the regional ALX train in the Czech Republic from an EX to an EC, you can no longer use the Bayern-Böhmen-Ticket on that train inside from the Czech Border to Pilsen. You can purchase a Bayern-Ticket, which will take you to the Czech border at Furth im Wald for 23€ (plus 5€ each added person). If you purchase a Czech Rail ticket from Furth i.W. to Prague (from www.cd.cz) for 391 Kc (~14.33€), that will cover the rest of the trip. Strangely, separate tickets from Furth i.W. to Domazlice (106 Kc=~3,89€) and from Domazlice to Prague (189 Kc=~6,93€) only add up to 10,82€.
So for a single person, the train is slightly more than the lowest priced bus ticket (if you purchase long enough in advance). For two people, the train costs 26€ + 5,60€ + 2 x 3,70€ or 39€ vs 58€ or more for the bus. A difference between the lowest fares is that you can always purchase the Bayern-Böhmen-Ticket just before travel, but the Europa-Spezial bus ticket requires advance purchase and might not be refundable. If you purchase the Bayern-Böhmen-Ticket at the Marienplatz station, it will cover the S-Bahn to the Hbf (except for weekdays before 9). If you purchase the bus ticket online, make sure you specify Munich, Marienplatz to Prague so your ticket will include the S-Bahn leg and you won't have to buy an additional S-Bahn ticket.