Zen Cart considers some warnings important enough to place them everywhere they might be needed. Since you have not answered the posting tips, I'll make some assumptions.
First of all, it appears you have upgraded without following the steps. Specifically updating the database to the current level. If you do not do this, you are subject to the cart not working. Thus, the reason the warning is in the cart.
Secondly, if you're concerned about a customer seeing this warning, you might be updating a live site.
Both are not advised.

You check the cart's operation right after upgrading, adding a mod, creating a new category/product or etc. right? Wouldn't you want to know immediately that would make the cart not operate.
What you are wanting to do is like turning off the overheat warning on your CPU.
I'd just fix the problem. Only takes seconds. http://www.zen-cart.com/content.php?...pgrade-my-site steps 8 thru 10