I'd almost say make that an option to strip anything after a ? or / per CoS or even per user basis. I would think some admins would want the securty of stripping the url and then others would want the functionality of showing the actual website. Most often if it is that specific of a website with session info ect, alexa isn't going to have a thumbnail of it anyways.
Also for the mouse hover url problem as a temporary solution you can disable "View mail as HTML (when possible)" in CoS preferences. This will make it show
instead of just
However this does require a client to log out and back in for the changes to take effect, and an user can override this setting in their preferences.
Edit added Bug 7315 for stripping URLs that are sent to alexa, http://bugzilla.zimbra.com/show_bug.cgi?id=7315