Nobody says the art needs to be kept there till end of universe. Also they could rotate them with the ones they show upstairs, ie during some thematic period instead of broad spectrum they have now. Obviously they'll probably never remove Night watch or Girl with a pearl earring (at least I hope so), but still a major temporary refresh could draw a lot of people.

Who says there won't be many more museums in 50 years? Or some other model which will result in more art being on display.

If Dutch culture budget gets in serious issues, they could finance museum survival also via sales of those.

The options what to do with it are almost endless and much better than just losing them.