Sorry, we don't quite follow what you mean? We don't have any ready method for scripting in your page to determine if the cart is empty, but you might be able to figure something out based on our mini-cart status display (although even this is an unofficial hack):
http://www.e-junkie.com/bb/topic/3086
If you're using our cart's built-in Shipping calculation, that will figure the Shipping fee automatically based on whatever items the buyer actually has in their cart at any given moment -- i.e., it will not retain any shipping added for items which the buyer has removed from their cart order:
http://www.e-junkie.com/ej/help.shipping.htm