Bus from Prague to Munich

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I would like to know if the student agency buses from Prague to Munich have on-board toilet?

Definitely, all the long-distance international routes buses are equipped with WC (http://jizdenky.studentagency.cz/web/important-informations/customer-service/).
Though there is a minimal chance that it won't work for whatever reason, but it more like 1 out of 100 chance. And even if it happens, then they tend to make bathroom stops once in a while. So there is nothing to worry

Which is  better or faster a bus from Prague to Munich or the train?

Which is  better or faster a bus from Prague to Munich or the train?

Well, let's consider pro & con. With the direct train it takes app. 6 hours, while buses depending on company travel in 5 to 5:40. So in terms of timing the difference isn't that essential, while in terms of comfort it really depends on people traveling - some would appreciate free Wi-Fi and drinks on board of a bus, while others - space of a train and rail travel experience.
Also it makes sense to look at a pricing of such journey. Standard fare for the bus is 750 CZK (app.30 EUR), with a promo offer and in advance purchase maybe you can get ticket a bit cheaper, like 500 CZK. While with the train option, as we noted in the other topic (http://europetrainsguide.com/forum/index.php/topic,227.msg1280.html#msg1280), you can basically travel for 12 EUR per person (around 50 EUR for four passengers).
As well it makes sense to consider your timing and desired dep/arr. time, since buses and trains run a bit differently within day and night.