DIY: Bose Touring Stereo (NON NAV) iPod Interface Upgrade: iSimple Media Gateway
Here's an option that shows going through the glove box. I know you have a nav and aren't installing this particular product but it gives you the idea about rearranging the iPod connection to the glove box. This diy looks a lot more complicated that it is and you prob wouldn't be pulling out the hole head unit anyway.
It's just an option that currently exists as there are no aftermarket locks that I know of. If you're keeping your 160GB iPod in there all the time it's a really good option and honestly probably easier to do than trying to create some type of locking mechanism for the center.
FWIW if you're more concerned about lookie loos, adding a lock to the center console might ignite their curiosity more so just because not many center consoles have them to begin with.