I don't worry about break-ins, because I don't bolt unnecessary crap on it during my day to day commute. I also put cheap molle bags on the panels, so when I do use the panels, I can throw things into the bag vs. spending time bolting things on it. Otherwise, the panels and bags are usually empty, and takes me literally minutes to fill up the bags.
Also, what I put in the bags are smaller things or odd shaped things, like winch controllers, tire deflators, tire inflator hose, first aid, dog hiking crap, or basically anything that won't kill me in an accident. NO sharp, heavy, or blunt instruments. I also added a cargo net to separate the cargo bay and the passenger bay, so in case the panels do want to try and kill me one day, its less likely in succeeding.
So in essence, the panels and cargo net act like a security device 99 percent of the time.
IF there was a way to utilize a cargo cover, I would probably buy it too........but I didn't let the lack of a cargo cover stop me from utilizing the molle panel to suit my needs either. The molle panel has a more valuable to me vs. the increased risk of theft.