It's unfortunate that they are stooping to petty remarks in passing. I myself wouldn't tolerate that ("Huh?" won't stop them.) I would ask them politely not to accuse you of anything you have not done and that they have no proof of.
I'm not sure you can convince anyone who doesn't want to be convinced that you're innocent. But that shouldn't stop you from proclaiming your innocence.
As others have stated, I think a conversation is in order. I don't know if your flatmates have regular meetings; if they do, put this on the agenda. If they don't, you can propose a meeting to discuss the problem of disappearing food. (Note, I don't say stolen. The thief/thieves might believe it's not really "stealing" but more like "borrowing", but 'forgetting' to replace it. That saves face.)
When you're together (not all need to be present) be careful how you approach the problem; don't imply anyone is lying. That only leads to defensiveness. Just start the gathering as a brainstorming session about disappearing food. Explain that some of your own food has gone missing, and give specific examples if you can, the more recent, the better (specifics give the appearance of truth.) If someone accuses you of lying, don't go on the defensive. Just maintain that you have not accused anyone because you don't know who is taking the food. You only know that
- food has gone missing, and
- some think you are responsible.
You don't really know if it's even a roommate doing so. It might be a friend of a roommate, who knows?
Maintain that you are not responsible, and ask that no one accuse you without evidence, just as you are accusing no one. Redirect to the issue: you're all there to try to come up a constructive way to solve the problem (personally I have never had this problem, so I have no good solution.) Food theft is a common problem in dorms; there are lots of articles on line about it, e.g. here and here. Avoid putting forth punitive solutions like adding laxatives to your food; if someone suggests it, say that you don't want to make anyone sick.
There might not be a solution. If you all agree, you might decide to install a camera, or keep your food in locked boxes in your rooms, or even to install a lock on your room door.
If the meeting goes well, great. If no solutions are offered or accepted, ask if a few of you should meet with the Resident Advisor, or whoever is in charge of solving difficult problems in the dorm.