Hi,
If you want to hide the message just for the case when you empty the cart, it will be very very complicated.
Hiding the message globally would not be a really good solution because if the customer wants to go to checkout and his cart is empty, he is redirected and this message is displayed. So removing it will make confusion.
You can empty your cart without having the message. It is just you are doing it in the checkout and so, you can't even show the checkout page with your cart is empty. I don't know if you see the all context.
So I don't know what to tell you.
Regards,
Jerome - Obsidev.com
HikaMarket & HikaSerial developer / HikaShop core dev team.
Also helping the HikaShop support team when having some time or couldn't sleep.
By the way, do not send me private message, use the "contact us" form instead.