Just set the default to 'no' and you won't get any requests, then specifically allow those sites you want to give access to the feature. I never have these problems on any of my (Android) devices. I use a few alternative browsers (Firefox/Fennec, Lightning, Privacy Browser) as I don't trust Chrome to do my bidding knowing it makes exceptions for Google-owned domains just like I would not trust Safari where it concerns my choices towards Apple-owned domains.
This is definitely a possibility, but if a feature has 90% malicious/bullshit use and 10% legitimate use then there's a good chance it should either be removed or disabled by default (so the iOS situation regarding web notifications is perfectly fine by me).
There was a time when a large amount of the email travelling the 'net was spam. I'm glad that the solution did not consist of removal of all email servers and clients. Inline images in web sites are (ab)used to show advertising, on many sites this accounts for the majority of use of this feature. Should this feature be removed from Safari for that reason?
For some category of web 'applications' notifications are a boon so it is good to have the possibility to use them. Apple is slow to implement it as it can be used to make web apps more competitive with native apps, something which they're not that keen on as native apps makes them a lot of money.
I think that's a poor analogy. Notification spam was invented because people weren't checking their spam folder. Those ppl are unlikely to open themselves up to an even more intrusive medium to deliver unwanted messages. Sure there will be usage cases for it, but not as the people selling mobile notification as a panacea, in fact I argue that it can do more damage than good in the long run.
It's like that creep you met at a night club who won't leave you alone with txt messages. Sure you were drunk but don't get mad when I don't reply.