You use a much smaller set of applications than web sites. Moreover, you usually vet your applications and do not run random stuff. Application developers build up trust over time.
Even if I want to use the web as hypertext + some Javascript for interactivity, every stupid web site can pull these shenanigans.
You use a much smaller set of applications than websites because websites exist.
You're imagining a world where the most popular dev environment goes away, and service providers decide to use HTML forms instead of forcing me to download an app every time I want to order a pizza. That world does not exist. The apps aren't going to go away, and your security model can't be, "people just won't install untrustworthy apps."
And put things in perspective here -- we're talking about a security vulnerability that allows port scanning primarily for fingerprinting purposes. A native app can not only port scan, it can literally just make POST requests to those open ports across separate domains. The security risks we're talking about are not even remotely equivocal.
Don't get me wrong, stuff like port-scanning should be fixed in web browsers. But even with these vulnerabilities, the web is still unquestionably the safest consumer-accessible application platform that we have today. Moving applications off of the web and back onto native platforms would be setting security back half a decade.
When someone comes to me and asks how they make their phone more secure and more private, the number one piece of advice I give them, every single time, is "avoid native apps and use websites instead. Don't install Facebook, use the website. Don't install random clicker games, browse them online instead."
The web has been a major asset in my quest to get friends and family not to install a bunch of random malware on their devices. Doubly so when you throw kids and younger users into the equation. I am eternally grateful that the web is advanced enough that people can join a Zoom meeting without installing Zoom on their computer.
Maybe that’s true for you, but if the modern web apps didn’t exist, most average people would be downloading dozens or hundreds of miscellaneous apps. “Oh, I want to order a pizza on my computer, time to download the Domino’s app.” And then now you have Domino’s ads running as daemons on your system.
Even if I want to use the web as hypertext + some Javascript for interactivity, every stupid web site can pull these shenanigans.