If you find you need to temporarily turn off your site or don't want to take orders for a short period there a few options you can use.
Turn off the buy buttons (in Catalog Setup / Order Button - set that to Never Display ) and leave the site open so you don't lose any ranking in the search engines and customers can still browse. Make sure you put a note on the site when you'll be accepting orders again.
OR, Set the site with a maintenance template. You would do this in the Template area. Select any one of the Maintenance or Coming Soon templates from the drop down menu then click APPLY.