In the late 90s the majority web of developers seemed to believe that the only proper way to link to a webpage was by running some messy JavaScript code
No, the majority didn't. Bad developers did stuff like this, and some are probably still using the same tricks right now.
The majority realised how stupid it was to do so, and therefore didn't create links like this.
I've seen some crazily bad website code in my time, include sites outputting their HTML using nothing but hard-coded document.write() calls. That doesn't mean the majority of developers were following suit.
Agreed, also I think it's naive to assume it's always the developers fault when something like this happens. (In the 90's) more often than not it was some douchebag marketer clamouring about people 'leaving' their site and convincing management to open new windows for outbound links.
There's always been a divide between what developers encourage, and what clients ask for and want. This is one of the better arguments FOR developers creating javascript-heavy single page sites (for themselves, or demos)... if they had to rely on their clients they'd probably be years behind the curve.
Most of the OP's points seem to be cherrypicked from the typical "don't do this" lists. Bad developers will be bad developers. By the time we can invent languages or softwares that turn bad developers into good developers, I think we will be ready to hang up our keyboards and pick up art.
Perhaps annoying websites that didn't use real links were more "memorable", because they caused issues and required workarounds. Personally, though, I've seen more of them that I would have liked to.
No, the majority didn't. Bad developers did stuff like this, and some are probably still using the same tricks right now.
The majority realised how stupid it was to do so, and therefore didn't create links like this.
I've seen some crazily bad website code in my time, include sites outputting their HTML using nothing but hard-coded document.write() calls. That doesn't mean the majority of developers were following suit.