I’m a bit confused by comments on this topic. Do sovereign countries not have the right anymore to decide their own laws and issue punishment when they’re not followed?

Some laws are bullshit and I commend everyone who decides to ignore them.

but if 4chan ignores them, that opens the door for other measures like delisting the site from search engines or blocking access to it from the UK (these two examples are taken from the article)

This has already happened to a number of sites and services, with some voluntarily blocking access from the UK. 4chan's approach is just a bit different in the way that they are waiting to get blocked instead of doing the blocking themselves. It sucks for citizens from the UK, but they are the ones that put the people in power who created those laws.

Like, to the people saying UK can’t do laws which apply to services which are merely accessible in the UK and have no physical presence there, do you also apply this logic to the GDPR, which works the same way?

This has also been the case already. There are a number of American websites that will just straight up deny you access if you visit them from a EU country. Some even cite GDPR as the reason for being blocked. I don't think it's the best solution, but I accept it because I wouldn't want to visit a site that cannot comply with it anyways.