Personally, I have never had anything one of my trucks. As a supervisor, I have had to fill out many a damage claim/safety report on those that have.
When I have had to use my racks as 'live storage' I would do much the same as others have stated. Either leave something obviously "un-racked" or leave the keys on the seat (that habit back then was to leave keys in ignitions). It was supposed to be understood throughout our field office that that meant "secure the vehicle for travel". The results were less than optimal.
The single most effective thing I found was a 'mindset'. I cannot think of how many times driving down the road I asked myself, "is my load secure" (pintle hitch closed, trailer chains & lights hooked up, & chain pins in place and locked, etc). the answer to this question should always be NO!
If you had to ask, you have to check!!! Period.
In my case, it was the rare occasion that I had not. Probably had something to do with me following a truck that had a 5000ft roll of 5/16 galv. steel guy strand (wire) fall off the back of it at 60mph. ........... Talk about a slinky! [scared]