First, do not panic at what I am about to tell you. Some people get real excited and it really is not that big of a deal. At least read all of my post before you faint.
Cherry seeds, like apple seeds, contain a poison, cyanide. They do not contain a lot of cyanide. A lot of fruit tree seeds contain some cyanide. You can eat a few and it won't hurt you. Your chickens can eat a few and it won't hurt them. They or you would have to eat a lot before there was any danger.
If your chickens forage under a fruit tree and get some seeds, no big deal. But if you make something that contains a lot of fruit and you have a lot of seeds, dispose of them in a way that the chickens cannot get to a big pile of them. For your purposes, freezing the fruit for the chickens, I'd suggest pitting them first. That way you don't have to wonder about how many is too much.
As far as your basic question, when processing a 15 week old rooster, I found a plum pit in its gizzard. A plum pit is a lot bigger than a cherry seed. Yours will not be harmed by eating something the size of a cherry pit.
