fei2010 - I'm not sure I understand the security concern. Conceptually it is no different from any other automatically-updating software system. This architecture enables us to quickly make available bug fixes and feature updates to our software.
Moreover, the code is downloaded only into your browser, not into your Zen Cart server.
We do our best to ensure that our software is safe and error-free. With over 250 users now, I would say that if we make mistakes in the security area, we'd be hauled up very quickly.
Please feel free to follow up with specific concerns you might have, and we will gladly respond.
Hope this helps.
Apsona
http://apsona.com