My Honda has a lockout that disables the lever used to open the trunk from the driver's seat. Of course, many cars have a fold down rear seat (mine doesn't) meaning any valet that really wants to check out your trunk will still be able to.
My 15 year old Honda has locks on all of those things, that you cannot unlock with the valet key. There is a lock on the trunk lever, a lock on the shelf in the back window for the seats, and a lock inside the armrest cubby in the back for the fold-down cup-holder stowaway door thinger.