Problem with running a lock through the frame is it allows a thief to use the frame as a lever. Sure the bike may be trashed when they get it, but they still have plenty of components to sell off at the flea market/swap meet/craigslist/etc.

True, you can still attempt to perform a leverage attack on a "sheldon locked" bike, but the thief is more likely to just pop the wheel out of the dropouts. Yes, your bike will still be mangled, but at least you have something that can be repaired, and not just buying a whole new bike (or spare parts if it costs too much to repair and you buy a new bike anyways).

It's a game of minimizing loss.