Is this really that big of a problem? You had to be expecting that local storage is deleted without any notice anyway, in every web app.
If Apple provided an alternative this would be ok. An alternative such as the native file access API (still a WIP). Or a prompt so that the user can allow long-term storage. Or supporting the web app manifest so that users confirm they want to "install" a web app, granting it greater permissions.
But they've offered no alternatives here, that I can see. They've determined that client-side web apps are simply not important.