I keep a Travel Wallet with all of my Point and Miles cards in it. I usually leave this on the desk in the Hotel as it has no cash or credit cards in it.

Well, One night it came up missing and after searching the entire Room and going though all of my luggage I was convinced that housekeeping had taken my wallet.

Two days later I was looking for the phone book and there was my wallet. In a Drawer in the nightstand. Housekeeping must have seen the wallet and put it in the drawer.

So, while I'm sure that in some hotels housekeeping does take things, that is not always the case when something is missing.