tldr: keep short term food at your desk. Offer alternative long term food (funded by the company or donations from coworkers) to protect your own long term food.
I see two separate problems here and they have different solutions.
First, you are preparing something at home, taking it to work, and putting it in the fridge to eat that day. After about 3 hours in the fridge, it's gone, and you don't get any lunch that day. This is pretty rare, really, and I recommend using an insulated bag on or near your desk and ignoring the fridge, while mentioning to management that it's a shame a labelled personal possession can be taken so quickly and blatantly.
Second, you keep something in the fridge or freezer that you might eat sometime soon. You use this when you are hungrier than you expected, or stay late. (Or perhaps one day you're less hungry than you thought, so you leave part of your lunch at work to eat the next day.) After a week or two in the fridge or freezer, you go to eat it and it's gone. This one is far more common. Someone with poor impulse control has convinced themselves they'll replace it before you notice, but has then forgotten. Sure, they should have left it, and failing that replaced it, but they have poor character. Shaming notes etc generally don't work.
I think your best bet here is to ask management for a small budget - say $10/week for a dozen people - and use that to buy fruit, the occasional box of Hot Pockets, and so on. These items will be clearly labelled "free for anyone" "help yourself" "company-provided snacks for people working late" and so on. Now instead of asking Mr Poor Impulse Control to sit hungry at his desk while perfectly yummy food (that he intends to replace) is just feet away, which he's shown he can't do, you're asking him to eat the free stuff and leave the private stuff alone, which he can probably do.
If management won't give you a budget, consider collecting a dollar a week from your coworkers (purely voluntarily of course) and taking turns doing the collecting and shopping. The convenience of knowing there's an apple in the breakroom, some muffins in the freezer etc, will be nice for all of you, and the confidence that anything special you've brought is more likely to be respected will also be nice.