This is going to be hit or miss and is up to the dealership. They will need to make the case to corporate if they wish to cover it. At John Deere, it was extremely hard to cover 3pt links under any warranty, why? Negligence.
3pt links are designed to lift and pull forwards. They are not designed for backhoes, or for pushing heavy loads in reverse (think pushing a rear blade in reverse dosing a pile of mud), but people do it. And a break is a break. "I'm sorry dear tractor owner." says the dealership mechanic, "But I just don't believe that they simply snapped. You did something you were not supposed to." Thats what they are thinking. When in fact, you could be absolutely correct, and have never abused them in the slightest. In the eyes of corporate (and some dealers), the burden of proof lies with you, and you must prove that its not negligence. Unfortunately, good luck with that.
Some might even consider the links to be separate from the tractor, as in an attachment, like the FEL. Even though the FEL is almost always connected to the tractor, its still separate. In fact, the links are easier to remove (on mine) than the FEL! I have even heard of a dealer calling the links (in this case it was the top link) a consumable, like your wiper blades!
But, a good dealer with a good reputation and in good standing with corporate could get them covered. But I wouldn't expect them to.
The warranty is a sales pitch, for everything. It's icing on the cake and is intentionally vague. It's to give you that warm fuzzy feeling that if anything goes wrong, its covered. Well, thats not completely accurate.