Yes, this is a problem when people code their websites against current iterations of a browser. It's not a problem regarding Chrome removing window.alert() but rather a problem that happened at development of the site, not at the iteration of browser (which is being discussed here)
> browsers are allowed to ignore those prompts
Unless previously marked as "Block future popups", is there any browser that currently (by default) doesn't block JS execution upon window.alert()? AFAIK, all browsers currently do.
> now they have to fix their code
Yeah, good luck maintaining the web with that mindset. There are countless of websites that will basically vanish (rather, stop working) if you change the execution model of browsers too much.
But large swaths of the web currently are just online because someone set it up well 20 years ago and has never touched it since. Maybe they can't even modify it at this point.
So any change needs to consider the historical impact the change can have. Hopefully the people working on browsers and standards have a bit better mindset than "now they have to fix their code", because otherwise we're utterly screwed.