What should a resturant do if people keep stealing their salt and pepper shakers?

Running a business inevitably has costs, especially if there’s a premises involved. People who enter your site are going to expect that there’s a bit of upkeep involved to keep the place running. You might use lights which require batteries or electricity; or have your own power source. You might decide to supply heating in the colder months; or you might decide to splash out and provide or build a table and chairs. All this equipment; including your precious pepper pots; will invoke some kind of cost which you will need to factor into your pricing when you calculate your overheads. If you’re concerned about your costs then you’ll have to put your prices up or at least challenge the people who enter or manage your premises to act accordingly. If they’re of sentimental value then consider using other methods of dispense.  Or if you can prove that someone’s done it and you’ve got their details you can report a case of theft to the police.