That's how itch.io is designed to work. There are ways to set the headers right, but I don't know how.
Let me try a different question: is there anything I can do as a developer to make localStorage work for players on iPad on itch.io?
I've got people complaining that they lost hours of progress :(
Yes, as I said, far as I know there's a way. It's just not the default, for security reasons. This is often discussed on the forum, so there should be someone here who knows the answer.