The trains run very frequently at that time of the day (maybe every 10 mins), so that would not be an obstacle. Just make sure you allow yourself enough time to get back for getting through check-in and security. You can buy your ticket from a vending machine and avoid the ticket windows. The Amsterdam Centraal rail station is quite a distance from the museum area, so you won't have time for those. When you exit the station, just walk straight ahead for about a half mile and you'll be at the start of the shopping district.

Another option is a quick tram tour, as there are a number of lines right outside the station.