Do you leave it on the water when not there or are you worried about it sitting at home?
Any thief worth his salt will get into anything you rig up if he wants to. The question is how much damage do you want him to cause doing it? While a cover isn’t much protection it does help with the spur of the moment guys. Out of sight out of mind.
I think the best thing you can do is inventory all your rods, reels, gear and take pictures. Send the photo file to you insurance agent to be kept in your file he has. Then if the unthinkable happens at least everybody knows what you lost. With todays camera phones this is easy and everybody should consider it.
Other than that I personally haven’t seen anything I thought would keep a thief out.