My Limited floor mats cover them and I think all OEM mats cover the bins.
It's still easy to access them and I would much rather they cover the bins as it provides a little more security. The typical crack head who breaks into your truck may not know those storage areas exist and may not find them if they are covered by a floor mat.
They will provide a little more security than the center console or glove box if you need to temporarily store something in your truck because the place you are visiting prohibits you from taking it with you.
I'm considering one of these for a little extra security.