The most expensive parts are the NXT or EV brick, the motors, sensors and batteries, so these need to be monitored closely.
Batteries should be charged in a lockable cupboard, too. You don't have to pull the battery out of the intelligent brick (brain) to charge. Assembled robots can still have their battery charged without removing it.
Use a permanent marker or sticker to number each group's main parts. Keep them in a seperate tub with the same number.
Ideally these parts should be kept in a locked cupboard.
Before each project make sure each group has all their main parts. Often I don't even give access to sensors that I know won't be used.
All the other bits and pieces can be stored in a separate big tub. Tip all these parts on a blanket or sheet at the start of a lesson, then it will be easy to pack up at the end.