As a locksmith and Vanagon owner, I, too, had the same problem.  I put a cam
lock in the spare battery compartment behind the driver's seat.  It's just a
$5 lock, but I could have used a better one.  My thoughts are that with the
carpet covering it, Nobody but a fellow Vanagon owner would know about it.
Just an idea.  Good luck.
Steve Sandlin
www.steveslockshop.com
'84 Wolfsburg Westy
'79 Transporter
'00 New Beetle