I believe that the panniers are really meant to be removed and then carried, rather than being left on the bike as they are held on by snap-on fasteners.If you were going to leave them on the bike I think you would have to fettle with them in some way to more securely attach them to the bike, or at the very least least pass a lock cable through them.
To be honest, when it comes to bikes and concerens about theft I'd think more about not making your bike stand out from the crowd when locked up. A cheaper pair of panniers that are more easily secured to the bike and of a more suitable and darker material - yep, waterproof plastic - would be a better choice IMHO.
That's what I ultimately decided. I'm going to just use a wooden crate and then can toss my filson tote or 257 into it for my office commute. This will then be my briefcase for the day. I prefer this to carrying panniers around (and its a whole lot cheaper).