Hi Andrew,
The Deleted/Deactivated Product being still able to be navigated to the product details page and purchased was a bug that was resolved in the release of version 5.45 back on 4/1/2013.
Setting the Quantity on Hand to zero will only prevent a user from purchasing if Inventory Management is enabled in your Store Settings. Please see the "Inventory Management" section in the KB article at the following link for more info:
http://helpdesk.smith-consulting.com/...
I recommend upgrading to the latest version of the Cart to take advantage of all the enhancements and bug fixes listed in our Change Log at the following link:
http://www.smith-consulting.com/Produ...
Let me know if I can help with anything else!