Ceský Krumlov 到 Salzburg

From experience - prices for trains trips crossing borders are never shown on the web pages. You'd have to go and ask at the train stations unfortunately. If you're in HK, you can check other guide books for a rough idea of the prices. I go by Lonely Planet guide books all the time (only because I'm more comfortable reading English.) I'm sure there are books in Chinese that would give a rough idea as well.
Hmm that looks like just a 6 hr train trip. It not so good to arrive in Salzburg after midnight if you don't know your way. Sure there are still some buses and taxis on the streets and can probably take you to your pre-booked hostel/hotel but it's just not too safe. There are alot of drunkens outside the train station. The tourist office and the rail offices are closed at that time. The ticket booths are still open, only one or two though.
There should be a day train from Cesky Krumlov to Salzburg - because it's only a 6 hr trip and can be done during the day. There should be quite regular services, not one train every hour but at least 1 train every 2 hours or so I'm guessing from my experiences. I suggest having another look. Otherwise you can stop over in Vienna for 1 day then move on to Salzburg but that's an extra ticket.
Hope that helps.