I kept my kayak on my rack for over two years with no problems.
It would have taken 4 guys to even attempt to steal the yak and rack. I have cable locks that connect to the bed, racks, kayak and my gear boxes. I'm sure that a determined thief could steal anything, but it would take some time. That's the case with everything, though. There are very few foolproof security measures; however, you can make it so difficult or time consuming the thief will look for an easier target.
Those rollers will make dents in the hull if the kayak sits on them for any length of time. Even the saddles can cause hull deformations. Either carry the kayak up-side-down or don't leave it on the rack for long.