items in my retail store are gone when I am not looking

@BudgiesAreBest Unless you have mods or cc that are increasing the behavior, I feel your pain and got really annoyed about this issue at one point. I owned a restaurant, and a guy would not leave when it closed and I noticed him steal a picture from the wall. Want to know my solution? I expect you have found, like me, that the same group of people tend to frequent your restaurant or store. If you no longer want to deal with this klepto problem you can try a few things:

Watch the store customers very closely....

• Hover over all customers and keep a list of their names.
• If you see the stealing happen your detective work will be easier. If you don't see it happen, start hunting down the offenders in the played/unplayed households in your game. 
• If you find someone who has the klepto trait you can:
  Delete them.
  Move them into their own household and just 'store them' in your library (taking them out of your played/unplayed households, but no need to delete them then. 
  Have your manager go after them with mean actions until the ability to fight comes up and beat the tar out of them (hopefully)? They may leave then. And you could do that if they return?
  Go into their lot and check their possessions/personal inventory for your item(s), confiscate them by creating a room, adding the items to the room, uploading the room to your library, and downloading it to the store lot and having your sim re-possess the item(s) (unfortunately it will cost you to do this).
  You could play the klepto sim and see if you can get them to visit your sim and gift the item(s) to them.
  If you see this happen you can exit the game without saving to go back to when the item was there>
  You can play the klepto sim and 're-trait' them (I have a 'retraiting potion' in my library in the gallery you could download and use, or you can do it by a cheat, I believe)

Anyway, those are a few of the possible ways to approach the kleptos in your store. If it is happening frequently maybe you have a few too many of them currently in your world (since the 'spawned' community sims are created randomly, maybe this dynamic just happened to make more than usual for your current game?) I play a tight ship in my sim households, and play pretty-much nice sims, so I do find that evil and klepto sims are very annoying to me. But... as you said, this also adds some realism if you like this. So maybe just cut back on how many. Have fun with your detective & vigilante work! (Too bad we can't call the police on them, huh? Also, you could make the suggestion to tone it back on this thread, if you like: https://forums.thesims.com/en_US/categories/the-sims-4-feedback)