I agree about clicking no all the time. This isn't an intractable problem, though; people just assume the ask-on-visit interaction pattern is the only way to implement this kind of functionality.

If I were on the Mobile Safari team, I'd propose bundling notifications into the bookmark workflow. If a user chooses to bookmark a site, prompt them at that moment (as an option in the modal) to subscribe to notifications if the site offers it. Because the user is expressing an interest in returning to the site, it's now appropriate to ask them to enable notifications, versus their first visit.

(For sites accessed through a synced iCloud bookmark, however, I would show a notifications prompt for the first visit on that device.)