I did quickly scan the burial entries at sv. Haštala for the 9 months prior to František's birth and did not find any entry for a Wenceslaus/Waclaw Nowak, or any Nowak for that matter. Could have missed something, though.
For Wenceslaus to be the father of Kateřyina I would have liked to see any indication of that in the "Parents" column. So I guess I would be inclined to believe hat Wenceslaus was the father.