If I didn't want to (or couldn't) take the night train (and after the two sleepers there is a midnight all seated alternative, several changes train) then I would without a doubt take the 9 hour day train straight through.
However in the hypothetical case that I wanted to break the day journey up it wouldn't be in Salzburg. Not because I don't like Salzburg, or I don't think it is a worthy place (the opposite is true), but it is only two hours into the 9 hour journey.
Personally my cholce of an overnight break of journey would therefore be Innsbruck because it is 4 hours from Vienna, so pretty much the mid point of the journey. The other benefit of that approach is that if the main line from Vienna to Salzburg was blocked for some reason there are two, three or four (depending how you count them) other (much) slower routes from Vienna to Innsbruck, avoiding Salzburg entirely.
Likewise between Salzburg and Innsbruck if that section was blocked then there is a slower route between the two cities.
So I would feel that all possible scenarios were covered.