I really prefer to go to Salzburg over Vienna (I've already been to both), but my quick research has shown it takes longer by train to get there from Prague, and we only have a half day and 1 night to spend at either place on our way to Venice. Can anyone tell me if it's really that much longer of a route and if it's worth the extra travel time for the amount of time we'd get to spend there?
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Skip the visit of Salzburg or Vienna. The time is too short, and the travel time too long.
There are cheap non-stop flights from Prague to Venice. For a random day in May I found a one-way flight for $40.
Search here: https://www.kayak.com/flights/