Pop up notifications can't be set as hidden... but yeah... I remember that I did a suggestion regarding this matter, because in the market auctions once you win an auction a notification emerges, and if you have a auction with a countdown going on, it's a bit annoying because you have to close the screen.
I would add a option to turn-off or have a minimalistic version of these notifications with a particular screen where to check them at the proper moment.
Even a small triangle icon sticky in a screen corner would be enough to let us know that there's a notification, and we could drag the icon or push it and open notifications instead.