Plenty of books have been set in Amsterdam, none scifi themed though, as far as I know. And none of the fictional books, usually written by 'foreigners' have ever struck me as particularly accurate. Maybe they got the places right, but never the atmosphere. To people who don't live here Amsterdam is either the city where anything is possible (except maybe anything scifi related) or the sodom and gommora of its day. And neither of those places is where I live.
Bearing that in mind, I don't take realistic settings in books that serious. I know that the author's view on a place is just one view, often tainted with theneed for the storyline. Which is great! But to go on a touristy tour with a book in my hand, like they did for books like that one with the Da Vinci stuff, nah.
However, it always warms my heart to see bits and pieces of Amsterdam in films. And I dont think it is likely that we'll ever see a spaceship hovering over Dam Square in any film. Though that would be cool.