I had V's carpeting do my boat and I had him pad the entire front deck. I'm sure he accounted for the padding but the locks work fine and now having done it, I won't ever have a boat without it! Makes all the difference in the world. And no, hooks don't catch it easier. It actually seems, if you use a heavier carpet, that the hooks don't catch AS easy....
'99 Skeeter 186SX SC, 150 Yamaha VMax
'13 Ford F-150 SCrew XLT, 4x4, 5.0, 6-spd