So my ADV model comes with the panniers and locks for both the contents and to lock the boxes to the carriers. Can't the carriers be removed from the bike quite easily? Doesn't this make the locks on the boxes largely useless?

You need these. Only pic I could find. Hope ebay link is ok.

SUZUKI V-STROM DL650 TOURING & ALUMINUM LUGGAGE SIDE CASES CARRIER LOCK SET | eBay

Yup - you've got it right. The locks keep honest people honest. But if you have a screwdriver, you can take the entire rack.

Same thing from Twisted: SW-MOTECH Keyed Locking Quick-Lock Fasteners (pair) - TwistedThrottle.com

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2012 DL650 EXP

Designed for outdoor use

Thanks guys. I'll put that on my Christmas gift wish list.