We would like to travel late night or mid night so we could stay a night in the train.
Well, there is an everyday overnight train (CNL40463) dep. Munich 23:36 and arriving to Venice 8:24 next morning. However it is not very cheap even if you purchase your tickets well in advance.
And what are the legit site for us to look since there are so many trains sites. We look into these two German/Austrian-run EuroCity trains, but still not sure.
When you aren't sure about which website to use for booking tickets - always go with the official website of the railway company that actually runs the train
In this case it will be already mention in the other topic
German Railways (DB)