I have rabbits too, and the rats are not allowed near them since one of my two rabbits is VERY grumpy about seeing the rats out and will box at them and try to bite if they get too close to his crate. But when the rabbits are put away, my rats love digging in their hay/litter boxes too. I think as long as it's cleaned everyday, it's probably fine. You might want to wash them off or wipe them with a wet towel afterwards to get urine residue off their fur that may have rubbed off on them. I'd also make sure they aren't nibbling the rabbit poop just to be safe. Keep an eye out for scabs on your rats. I once bought hay for my rabbits at a new location, and all my animals got mites/lice and had to be treated. They love digging in the hay though! I've added hay to their cages in a basket a few times and they're happy. I think it's probably fine though for your rats to go digging!
