Uppsala Nya Tidning's articles "Presidentbesök i Uppsala
" and "Presidentbesök i Enköping
" doesn't mention any royals and they were not mentioned in the County Administrative Board's press information about the visit.
That the King, Queen and Crown Princess attended events of the state visit during two days is a lot already, plus Prince Carl Philip and Princess Madeleine on the first day's gala banquet. They usually don't attend all three days of activities, there's always a big part of the schedule that is only for the visiting head of state and entourage (most of it political meetings, but this time they scheduled a lot of that for the President on the first day).
About the visit to the Vasa Museum and The Museum of National Antiquities, I guess they may have wanted a little break to prepare for the evening's concert and reception... Just a guess though, maybe the King had some office work to do as well. And the Vasa Museum is really what the Munk Museum is for Queen Sonja of Norway - King Carl Gustaf and Queen Silvia can probably give a tour of it in their sleep by now